The Enzyme Database

Your query returned 50 entries.    printer_iconPrintable version



EC 1.1.5.6      
Transferred entry: formate dehydrogenase-N. Now EC 1.17.5.3, formate dehydrogenase-N
[EC 1.1.5.6 created 2010, deleted 2017]
 
 
EC 1.2.5.1     
Accepted name: pyruvate dehydrogenase (quinone)
Reaction: pyruvate + ubiquinone + H2O = acetate + CO2 + ubiquinol
Other name(s): pyruvate dehydrogenase (ambiguous); pyruvic dehydrogenase (ambiguous); pyruvic (cytochrome b1) dehydrogenase (incorrect); pyruvate:ubiquinone-8-oxidoreductase; pyruvate oxidase (ambiguous); pyruvate dehydrogenase (cytochrome) (incorrect)
Systematic name: pyruvate:ubiquinone oxidoreductase
Comments: Flavoprotein (FAD) [1]. This bacterial enzyme is located on the inner surface of the cytoplasmic membrane and coupled to the respiratory chain via ubiquinone [2,3]. Does not accept menaquinone. Activity is greatly enhanced by lipids [4,5,6]. Requires thiamine diphosphate [7]. The enzyme can also form acetoin [8].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Recny, M.A. and Hager, L.P. Reconstitution of native Escherichia coli pyruvate oxidase from apoenzyme monomers and FAD. J. Biol. Chem. 257 (1982) 12878–12886. [PMID: 6752142]
2.  Cunningham, C.C. and Hager, L.P. Reactivation of the lipid-depleted pyruvate oxidase system from Escherichia coli with cell envelope neutral lipids. J. Biol. Chem. 250 (1975) 7139–7146. [PMID: 1100621]
3.  Koland, J.G., Miller, M.J. and Gennis, R.B. Reconstitution of the membrane-bound, ubiquinone-dependent pyruvate oxidase respiratory chain of Escherichia coli with the cytochrome d terminal oxidase. Biochemistry 23 (1984) 445–453. [PMID: 6367818]
4.  Grabau, C. and Cronan, J.E., Jr. In vivo function of Escherichia coli pyruvate oxidase specifically requires a functional lipid binding site. Biochemistry 25 (1986) 3748–3751. [PMID: 3527254]
5.  Wang, A.Y., Chang, Y.Y. and Cronan, J.E., Jr. Role of the tetrameric structure of Escherichia coli pyruvate oxidase in enzyme activation and lipid binding. J. Biol. Chem. 266 (1991) 10959–10966. [PMID: 2040613]
6.  Chang, Y.Y. and Cronan, J.E., Jr. Sulfhydryl chemistry detects three conformations of the lipid binding region of Escherichia coli pyruvate oxidase. Biochemistry 36 (1997) 11564–11573. [DOI] [PMID: 9305946]
7.  O'Brien, T.A., Schrock, H.L., Russell, P., Blake, R., 2nd and Gennis, R.B. Preparation of Escherichia coli pyruvate oxidase utilizing a thiamine pyrophosphate affinity column. Biochim. Biophys. Acta 452 (1976) 13–29. [DOI] [PMID: 791368]
8.  Bertagnolli, B.L. and Hager, L.P. Role of flavin in acetoin production by two bacterial pyruvate oxidases. Arch. Biochem. Biophys. 300 (1993) 364–371. [DOI] [PMID: 8424670]
[EC 1.2.5.1 created 2010]
 
 
EC 1.3.5.1     
Accepted name: succinate dehydrogenase
Reaction: succinate + a quinone = fumarate + a quinol
For diagram of the citric acid cycle, click here
Other name(s): succinate dehydrogenase (quinone); succinate dehydrogenase (ubiquinone); succinic dehydrogenase; complex II (ambiguous); succinate dehydrogenase complex; SDH (ambiguous); succinate:ubiquinone oxidoreductase
Systematic name: succinate:quinone oxidoreductase
Comments: A flavoprotein (FAD) complex containing iron-sulfur centres. The enzyme is found in the inner mitochondrial membrane in eukaryotes and the plasma membrane of many aerobic or facultative bacteria and archaea. It catalyses succinate oxidation in the citric acid cycle and transfers the electrons to quinones in the membrane, thus constituting a part of the aerobic respiratory chain (known as complex II). In vivo the enzyme uses the quinone found in the organism - eukaryotic enzymes utilize ubiquinone, bacterial enzymes utilize ubiquinone or menaquinone, and archaebacterial enzymes from the Sulfolobus genus use caldariellaquinone. cf. EC 1.3.5.4, fumarate reductase (quinol).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-11-9
References:
1.  Kita, K., Vibat, C.R., Meinhardt, S., Guest, J.R. and Gennis, R.B. One-step purification from Escherichia coli of complex II (succinate: ubiquinone oxidoreductase) associated with succinate-reducible cytochrome b556. J. Biol. Chem. 264 (1989) 2672–2677. [PMID: 2644269]
2.  Hatefi, Y., Ragan, C.I. and Galante, Y.M. The enzymes and the enzyme complexes of the mitochondrial oxidative phosphorylation system. In: Martonosi, A. (Ed.), The Enzymes of Biological Membranes, 2nd edn, vol. 4, Plenum Press, New York, 1985, pp. 1–70.
3.  Moll, R. and Schafer, G. Purification and characterisation of an archaebacterial succinate dehydrogenase complex from the plasma membrane of the thermoacidophile Sulfolobus acidocaldarius. Eur. J. Biochem. 201 (1991) 593–600. [DOI] [PMID: 1935955]
4.  Figueroa, P., Leon, G., Elorza, A., Holuigue, L., Araya, A. and Jordana, X. The four subunits of mitochondrial respiratory complex II are encoded by multiple nuclear genes and targeted to mitochondria in Arabidopsis thaliana. Plant Mol. Biol. 50 (2002) 725–734. [PMID: 12374303]
5.  Cecchini, G. Function and structure of complex II of the respiratory chain. Annu. Rev. Biochem. 72 (2003) 77–109. [DOI] [PMID: 14527321]
6.  Oyedotun, K.S. and Lemire, B.D. The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies. J. Biol. Chem. 279 (2004) 9424–9431. [DOI] [PMID: 14672929]
7.  Kurokawa, T. and Sakamoto, J. Purification and characterization of succinate:menaquinone oxidoreductase from Corynebacterium glutamicum. Arch. Microbiol. 183 (2005) 317–324. [DOI] [PMID: 15883782]
[EC 1.3.5.1 created 1983 (EC 1.3.99.1 created 1961, incorporated 2014)]
 
 
EC 1.3.5.3     
Accepted name: protoporphyrinogen IX dehydrogenase (quinone)
Reaction: protoporphyrinogen IX + 3 quinone = protoporphyrin IX + 3 quinol
Other name(s): HemG; protoporphyrinogen IX dehydrogenase (menaquinone)
Systematic name: protoporphyrinogen IX:quinone oxidoreductase
Comments: Contains FMN. The enzyme participates in heme b biosynthesis. In the bacterium Escherichia coli it interacts with either ubiquinone or menaquinone, depending on whether the organism grows aerobically or anaerobically.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Boynton, T.O., Daugherty, L.E., Dailey, T.A. and Dailey, H.A. Identification of Escherichia coli HemG as a novel, menadione-dependent flavodoxin with protoporphyrinogen oxidase activity. Biochemistry 48 (2009) 6705–6711. [DOI] [PMID: 19583219]
2.  Möbius, K., Arias-Cartin, R., Breckau, D., Hännig, A.L., Riedmann, K., Biedendieck, R., Schroder, S., Becher, D., Magalon, A., Moser, J., Jahn, M. and Jahn, D. Heme biosynthesis is coupled to electron transport chains for energy generation. Proc. Natl. Acad. Sci. USA 107 (2010) 10436–10441. [PMID: 20484676]
[EC 1.3.5.3 created 2010, modified 2020]
 
 
EC 1.3.5.4     
Accepted name: fumarate reductase (quinol)
Reaction: succinate + a quinone = fumarate + a quinol
Other name(s): FRD; menaquinol-fumarate oxidoreductase; succinate dehydrogenase (menaquinone); succinate:menaquinone oxidoreductase; fumarate reductase (menaquinone); complex II (ambiguous)
Systematic name: succinate:quinone oxidoreductase
Comments: The enzyme, which is found in anaerobic and facultative organisms such as bacteria, parasitic helminthes, and lower marine organisms, utilizes low potential quinols, such as menaquinol and rhodoquinol, to reduce fumarate as the final step of an anaerobic respiratory chain. The enzyme is known as complex II of the electron transfer chain, similarly to EC 1.3.5.1, succinate dehydrogenase (quinone), to which it is closely related.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Van Hellemond, J.J. and Tielens, A.G. Expression and functional properties of fumarate reductase. Biochem. J. 304 (1994) 321–331. [PMID: 7998964]
2.  Iverson, T.M., Luna-Chavez, C., Cecchini, G. and Rees, D.C. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284 (1999) 1961–1966. [DOI] [PMID: 10373108]
3.  Cecchini, G., Schroder, I., Gunsalus, R.P. and Maklashina, E. Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta 1553 (2002) 140–157. [DOI] [PMID: 11803023]
4.  Iverson, T.M., Luna-Chavez, C., Croal, L.R., Cecchini, G. and Rees, D.C. Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J. Biol. Chem. 277 (2002) 16124–16130. [DOI] [PMID: 11850430]
5.  van Hellemond, J.J., van der Klei, A., van Weelden, S.W. and Tielens, A.G. Biochemical and evolutionary aspects of anaerobically functioning mitochondria. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 (2003) 205. [DOI] [PMID: 12594928]
[EC 1.3.5.4 created 2010, modified 2013]
 
 
EC 1.3.99.38     
Accepted name: menaquinone-9 β-reductase
Reaction: menaquinone-9 + reduced acceptor = β-dihydromenaquinone-9 + acceptor
For diagram of vitamin K biosynthesis, click here
Glossary: β-dihydromenaquinone-9 = MK-9(II-H2) = 2-methyl-3-[(2E,10E,14E,18E,22E,26E,30E,33E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,10,14,18,22,26,30,33-octaen-1-yl]naphthalene-1,4-dione
Other name(s): MenJ
Systematic name: menaquinone-9 oxidoreductase (β-dihydromenaquinone-9-forming)
Comments: The enzyme from the bacterium Mycobacterium tuberculosis reduces the β-isoprene unit of menaquinone-9, forming the predominant form of menaquinone found in mycobacteria. Contains FAD.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Upadhyay, A., Fontes, F.L., Gonzalez-Juarrero, M., McNeil, M.R., Crans, D.C., Jackson, M. and Crick, D.C. Partial saturation of menaquinone in Mycobacterium tuberculosis: function and essentiality of a novel reductase, MenJ. ACS Cent. Sci. 1 (2015) 292–302. [DOI] [PMID: 26436137]
[EC 1.3.99.38 created 2017]
 
 
EC 1.6.5.10     
Accepted name: NADPH dehydrogenase (quinone)
Reaction: NADPH + H+ + a quinone = NADP+ + a quinol
Other name(s): reduced nicotinamide adenine dinucleotide phosphate (quinone) dehydrogenase; NADPH oxidase; NADPH2 dehydrogenase (quinone)
Systematic name: NADPH:(quinone-acceptor) oxidoreductase
Comments: A flavoprotein [1, 2]. The enzyme from Escherichia coli is specific for NADPH and is most active with quinone derivatives and ferricyanide as electron acceptors [3]. Menaquinone can act as acceptor. The enzyme from hog liver is inhibited by dicoumarol and folic acid derivatives but not by 2,4-dinitrophenol [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-37-4
References:
1.  Koli, A.K., Yearby, C., Scott, W. and Donaldson, K.O. Purification and properties of three separate menadione reductases from hog liver. J. Biol. Chem. 244 (1969) 621–629. [PMID: 4388793]
2.  Hayashi, M., Hasegawa, K., Oguni, Y. and Unemoto, T. Characterization of FMN-dependent NADH-quinone reductase induced by menadione in Escherichia coli. Biochim. Biophys. Acta 1035 (1990) 230–236. [DOI] [PMID: 2118386]
3.  Hayashi, M., Ohzeki, H., Shimada, H. and Unemoto, T. NADPH-specific quinone reductase is induced by 2-methylene-4-butyrolactone in Escherichia coli. Biochim. Biophys. Acta 1273 (1996) 165–170. [DOI] [PMID: 8611590]
[EC 1.6.5.10 created 1972 as EC 1.6.99.6, transferred 2011 to EC 1.6.5.10]
 
 
EC 1.6.5.11      
Deleted entry: NADH dehydrogenase (quinone). Identical to EC 1.6.5.9, NADH:quinone reductase (non-electrogenic)
[EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11, deleted 2019]
 
 
EC 1.6.99.5      
Transferred entry: NADH dehydrogenase (quinone). Transferred to EC 1.6.5.11, NADH dehydrogenase (quinone)
[EC 1.6.99.5 created 1972, deleted 2014]
 
 
EC 1.6.99.6      
Transferred entry: NADPH dehydrogenase (quinone). Now EC 1.6.5.10, NADPH dehydrogenase (quinone)
[EC 1.6.99.6 created 1972, deleted 2011]
 
 
EC 1.7.5.2     
Accepted name: nitric oxide reductase (menaquinol)
Reaction: 2 nitric oxide + menaquinol = nitrous oxide + menaquinone + H2O
Comments: Contains copper.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cramm, R., Pohlmann, A. and Friedrich, B. Purification and characterization of the single-component nitric oxide reductase from Ralstonia eutropha H16. FEBS Lett. 460 (1999) 6–10. [DOI] [PMID: 10571051]
2.  Suharti, Strampraad, M.J., Schroder, I. and de Vries, S. A novel copper A containing menaquinol NO reductase from Bacillus azotoformans. Biochemistry 40 (2001) 2632–2639. [DOI] [PMID: 11327887]
3.  Suharti, Heering, H.A. and de Vries, S. NO reductase from Bacillus azotoformans is a bifunctional enzyme accepting electrons from menaquinol and a specific endogenous membrane-bound cytochrome c551. Biochemistry 43 (2004) 13487–13495. [DOI] [PMID: 15491156]
[EC 1.7.5.2 created 2011]
 
 
EC 1.8.5.3     
Accepted name: respiratory dimethylsulfoxide reductase
Reaction: dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol
For diagram of dimethyl sulfide catabolism, click here
Other name(s): dmsABC (gene names); DMSO reductase (ambiguous); dimethylsulfoxide reductase (ambiguous)
Systematic name: dimethyl sulfide:menaquinone oxidoreductase
Comments: The enzyme participates in bacterial electron transfer pathways in which dimethylsulfoxide (DMSO) is the terminal electron acceptor. It is composed of three subunits - DmsA contains a bis(guanylyl molybdopterin) cofactor and a [4Fe-4S] cluster, DmsB is an iron-sulfur protein, and DmsC is a transmembrane protein that anchors the enzyme and accepts electrons from the quinol pool. The electrons are passed through DmsB to DmsA and on to DMSO. The enzyme can also reduce pyridine-N-oxide and trimethylamine N-oxide to the corresponding amines with lower activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Daruwala, R. and Meganathan, R. Dimethyl sulfoxide reductase is not required for trimethylamine N-oxide reduction in Escherichia coli. FEMS Microbiol. Lett. 67 (1991) 255–259. [PMID: 1769531]
2.  Miguel, L. and Meganthan, R. Electron donors and the quinone involved in dimethyl sulfoxide reduction in Escherichia coli. Curr. Microbiol. 22 (1991) 109–115.
3.  Simala-Grant, J.L. and Weiner, J.H. Kinetic analysis and substrate specificity of Escherichia coli dimethyl sulfoxide reductase. Microbiology 142 (1996) 3231–3239. [DOI] [PMID: 8969520]
4.  Rothery, R.A., Trieber, C.A. and Weiner, J.H. Interactions between the molybdenum cofactor and iron-sulfur clusters of Escherichia coli dimethylsulfoxide reductase. J. Biol. Chem. 274 (1999) 13002–13009. [DOI] [PMID: 10224050]
[EC 1.8.5.3 created 2011, modified 2019]
 
 
EC 1.8.5.4     
Accepted name: bacterial sulfide:quinone reductase
Reaction: n HS- + n quinone = polysulfide + n quinol
Other name(s): sqr (gene name); sulfide:quinone reductase (ambiguous); sulfide:quinone oxidoreductase
Systematic name: sulfide:quinone oxidoreductase (polysulfide-producing)
Comments: Contains FAD. Ubiquinone, plastoquinone or menaquinone can act as acceptor in different species. In some organisms the enzyme catalyses the formation of sulfur globules. It repeats the catalytic cycle without releasing the product, producing a polysulfide of up to 10 sulfur atoms. The reaction stops when the maximum length of the polysulfide that can be accommodated in the sulfide oxidation pocket is achieved. The enzyme also plays an important role in anoxygenic bacterial photosynthesis. cf. EC 1.8.5.8, sulfide quinone oxidoreductase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Arieli, B., Shahak, Y., Taglicht, D., Hauska, G. and Padan, E. Purification and characterization of sulfide-quinone reductase, a novel enzyme driving anoxygenic photosynthesis in Oscillatoria limnetica. J. Biol. Chem. 269 (1994) 5705–5711. [PMID: 8119908]
2.  Reinartz, M., Tschape, J., Bruser, T., Truper, H.G. and Dahl, C. Sulfide oxidation in the phototrophic sulfur bacterium Chromatium vinosum. Arch. Microbiol. 170 (1998) 59–68. [PMID: 9639604]
3.  Nubel, T., Klughammer, C., Huber, R., Hauska, G. and Schutz, M. Sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium Aquifex aeolicus (VF5). Arch. Microbiol. 173 (2000) 233–244. [PMID: 10816041]
4.  Brito, J.A., Sousa, F.L., Stelter, M., Bandeiras, T.M., Vonrhein, C., Teixeira, M., Pereira, M.M. and Archer, M. Structural and functional insights into sulfide:quinone oxidoreductase. Biochemistry 48 (2009) 5613–5622. [DOI] [PMID: 19438211]
5.  Cherney, M.M., Zhang, Y., Solomonson, M., Weiner, J.H. and James, M.N. Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification. J. Mol. Biol. 398 (2010) 292–305. [DOI] [PMID: 20303979]
6.  Marcia, M., Langer, J.D., Parcej, D., Vogel, V., Peng, G. and Michel, H. Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase. Biochim. Biophys. Acta 1798 (2010) 2114–2123. [DOI] [PMID: 20691146]
7.  Xin, Y., Liu, H., Cui, F., Liu, H. and Xun, L. Recombinant Escherichia coli with sulfide:quinone oxidoreductase and persulfide dioxygenase rapidly oxidises sulfide to sulfite and thiosulfate via a new pathway. Environ. Microbiol. 18 (2016) 5123–5136. [PMID: 27573649]
[EC 1.8.5.4 created 2011, modified 2017, modified 2019]
 
 
EC 1.10.2.2      
Transferred entry: quinol—cytochrome-c reductase. Now EC 7.1.1.8, quinol—cytochrome-c reductase
[EC 1.10.2.2 created 1978, modified 2013, deleted 2018]
 
 
EC 1.10.3.12      
Transferred entry: menaquinol oxidase (H+-transporting). Now EC 7.1.1.5, menaquinol oxidase (H+-transporting)
[EC 1.10.3.12 created 2011, deleted 2018]
 
 
EC 1.12.5.1     
Accepted name: hydrogen:quinone oxidoreductase
Reaction: H2 + menaquinone = menaquinol
Glossary: methyl viologen = 1,1′-dimethyl-4,4′-bipyridine-1,1′-diium
benzyl viologen = 1,1′-dibenzyl-4,4′-bipyridine-1,1′-diium
Other name(s): hydrogen-ubiquinone oxidoreductase; hydrogen:menaquinone oxidoreductase; membrane-bound hydrogenase; quinone-reactive Ni/Fe-hydrogenase
Systematic name: hydrogen:quinone oxidoreductase
Comments: Contains nickel, iron-sulfur clusters and cytochrome b. Also catalyses the reduction of water-soluble quinones (e.g. 2,3-dimethylnaphthoquinone) or viologen dyes (benzyl viologen or methyl viologen).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 151616-65-8
References:
1.  Dross, F., Geisler, V., Lenger, R., Theis, F., Krafft, T., Fahrenholz, F., Kojro, E. , Duchêne, A., Tripier, D., Juvenal, K. and Kröger, A. The quinone-reactive Ni/Fe-hydrogenase of Wolinella succinogenes. Eur. J. Biochem. 206 (1992) 93–102. [DOI] [PMID: 1587288]
2.  Dross, F., Geisler, V., Lenger, R., Theis, F., Krafft, T., Fahrenholz, F., Kojro, E., Duchene, A., Tripier, D. and Juvenal, K. Erratum to "The quinone-reactive Ni/Fe-hydrogenase of Wolinella succinogenes". Eur. J. Biochem. 214 (1993) 949–950. [DOI] [PMID: 8319698]
3.  Gross, R., Simon, J., Lancaster, C.R.D. and Kroger, A. Identification of histidine residues in Wolinella succinogenes hydrogenase that are essential for menaquinone reduction by H-2. Mol. Microbiol. 30 (1998) 639–646. [DOI] [PMID: 9822828]
4.  Bernhard, M., Benelli, B., Hochkoeppler, A., Zannoni, D. and Friedrich, B. Functional and structural role of the cytochrome b subunit of the membrane-bound hydrogenase complex of Alcaligenes eutrophus H16. Eur. J. Biochem. 248 (1997) 179–186. [DOI] [PMID: 9310376]
5.  Ferber, D.M. and Maier, R.J. Hydrogen-ubiquinone oxidoreductase activity by the Bradyrhizobium japonicum membrane-bound hydrogenase. FEMS Microbiol. Lett. 110 (1993) 257–264. [DOI] [PMID: 8354459]
6.  Ishii, M., Omori, T., Igarashi, Y., Adachi, O., Ameyama, M. and Kodama, T. Methionaquinone is a direct natural electron-acceptor for the membrane-bound hydrogenase in Hydrogenobacter thermophilus strain TK-6. Agric. Biol. Chem. 55 (1991) 3011–3016.
[EC 1.12.5.1 created 1999 as EC 1.12.99.3, transferred 2002 to EC 1.12.5.1]
 
 
EC 1.14.13.194      
Transferred entry: phylloquinone ω-hydroxylase. Now EC 1.14.14.78, phylloquinone ω-hydroxylase
[EC 1.14.13.194 created 2014, deleted 2018]
 
 
EC 1.14.14.78     
Accepted name: phylloquinone ω-hydroxylase
Reaction: phylloquinone + [reduced NADPH—hemoprotein reductase] + O2 = ω-hydroxyphylloquinone + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of vitamin K biosynthesis, click here
Other name(s): vitamin K1 ω-hydroxylase; CYP4F2; CYP4F11
Systematic name: phylloquinone,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (ω-hydroxyphylloquinone-forming)
Comments: A cytochrome P-450 (heme-thiolate) protein. Isolated from human tissue. The enzyme will also act on menaquinone-4. Prolonged action of CYP4F2, but not CYP4F11, on the ω hydroxyl group oxidizes it to the corresponding carboxylic acid. CYP4F2 also oxidizes leukotriene B4; see EC 1.14.13.30, leukotriene-B4 20-monooxygenase [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Jin, R., Koop, D.R., Raucy, J.L. and Lasker, J.M. Role of human CYP4F2 in hepatic catabolism of the proinflammatory agent leukotriene B4. Arch. Biochem. Biophys. 359 (1998) 89–98. [DOI] [PMID: 9799565]
2.  Tang, Z., Salamanca-Pinzon, S.G., Wu, Z.L., Xiao, Y. and Guengerich, F.P. Human cytochrome P450 4F11: heterologous expression in bacteria, purification, and characterization of catalytic function. Arch. Biochem. Biophys. 494 (2010) 86–93. [DOI] [PMID: 19932081]
3.  Edson, K.Z., Prasad, B., Unadkat, J.D., Suhara, Y., Okano, T., Guengerich, F.P. and Rettie, A.E. Cytochrome P450-dependent catabolism of vitamin K: ω-hydroxylation catalyzed by human CYP4F2 and CYP4F11. Biochemistry 52 (2013) 8276–8285. [DOI] [PMID: 24138531]
[EC 1.14.14.78 created 2014 as EC 1.14.13.194, transferred 2018 to EC 1.14.14.78]
 
 
EC 1.14.15.27     
Accepted name: β-dihydromenaquinone-9 ω-hydroxylase
Reaction: β-dihydromenaquinone-9 + 2 reduced ferredoxin [iron-sulfur] cluster + O2 = ω-hydroxy-β-dihydromenaquinone-9 + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
For diagram of vitamin K biosynthesis, click here
Glossary: β-dihydromenaquinone-9 = MK-9(II-H2) = 2-methyl-3-[(2E,10E,14E,18E,22E,26E,30E,33E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,10,14,18,22,26,30,33-octaen-1-yl]naphthalene-1,4-dione
Other name(s): cyp128 (gene name)
Systematic name: β-dihydromenaquinone-9,reduced ferredoxin:oxygen oxidoreductase (ω-hydroxylating)
Comments: The bacterial cytochrome P-450 enzyme is involved in the biosynthesis of ω-sulfo-β-dihydromenaquinone-9 by members of the Mycobacterium tuberculosis complex.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Holsclaw, C.M., Sogi, K.M., Gilmore, S.A., Schelle, M.W., Leavell, M.D., Bertozzi, C.R. and Leary, J.A. Structural characterization of a novel sulfated menaquinone produced by stf3 from Mycobacterium tuberculosis. ACS Chem. Biol. 3 (2008) 619–624. [PMID: 18928249]
2.  Sogi, K.M., Holsclaw, C.M., Fragiadakis, G.K., Nomura, D.K., Leary, J.A. and Bertozzi, C.R. Biosynthesis and regulation of sulfomenaquinone, a metabolite associated with virulence in Mycobacterium tuberculosis. ACS Infect Dis 2 (2016) 800–806. [PMID: 27933784]
[EC 1.14.15.27 created 2018]
 
 
EC 1.17.4.4     
Accepted name: vitamin-K-epoxide reductase (warfarin-sensitive)
Reaction: (1) phylloquinone + a protein with a disulfide bond + H2O = 2,3-epoxyphylloquinone + a protein with reduced L-cysteine residues
(2) phylloquinol + a protein with a disulfide bond = phylloquinone + a protein with reduced L-cysteine residues
For diagram of the vitamin K cycle, click here
Glossary: phylloquinone = vitamin K1 = 2-methyl-3-phytyl-1,4-naphthoquinone
2,3-epoxyphylloquinone = vitamin K1 2,3-epoxide = 2,3-epoxy-2-methyl-3-phytyl-2,3-dihydro-1,4-naphthoquinone
Other name(s): VKORC1 (gene name); VKORC1L1 (gene name)
Systematic name: phylloquinone:disulfide oxidoreductase
Comments: The enzyme catalyses the reduction of vitamin K 2,3-epoxide, which is formed by the activity of EC 4.1.1.90, peptidyl-glutamate 4-carboxylase, back to its phylloquinol active form. The enzyme forms a tight complex with EC 5.3.4.1, protein disulfide-isomerase, which transfers the required electrons from newly-synthesized proteins by catalysing the formation of disulfide bridges. The enzyme acts on the epoxide forms of both phylloquinone (vitamin K1) and menaquinone (vitamin K2). Inhibited strongly by (S)-warfarin and ferulenol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 55963-40-1
References:
1.  Whitlon, D.S., Sadowski, J.A. and Suttie, J.W. Mechanism of coumarin action: significance of vitamin K epoxide reductase inhibition. Biochemistry 17 (1978) 1371–1377. [PMID: 646989]
2.  Lee, J.L. and Fasco, M.J. Metabolism of vitamin K and vitamin K 2,3-epoxide via interaction with a common disulfide. Biochemistry 23 (1984) 2246–2252. [PMID: 6733086]
3.  Mukharji, I. and Silverman, R.B. Purification of a vitamin K epoxide reductase that catalyzes conversion of vitamin K 2,3-epoxide to 3-hydroxy-2-methyl-3-phytyl-2,3-dihydronaphthoquinone. Proc. Natl. Acad. Sci. USA 82 (1985) 2713–2717. [DOI] [PMID: 3857611]
4.  Li, T., Chang, C.Y., Jin, D.Y., Lin, P.J., Khvorova, A. and Stafford, D.W. Identification of the gene for vitamin K epoxide reductase. Nature 427 (2004) 541–544. [PMID: 14765195]
5.  Wajih, N., Hutson, S.M. and Wallin, R. Disulfide-dependent protein folding is linked to operation of the vitamin K cycle in the endoplasmic reticulum. A protein disulfide isomerase-VKORC1 redox enzyme complex appears to be responsible for vitamin K1 2,3-epoxide reduction. J. Biol. Chem. 282 (2007) 2626–2635. [PMID: 17124179]
6.  Spohn, G., Kleinridders, A., Wunderlich, F.T., Watzka, M., Zaucke, F., Blumbach, K., Geisen, C., Seifried, E., Muller, C., Paulsson, M., Bruning, J.C. and Oldenburg, J. VKORC1 deficiency in mice causes early postnatal lethality due to severe bleeding. Thromb Haemost 101 (2009) 1044–1050. [PMID: 19492146]
7.  Schulman, S., Wang, B., Li, W. and Rapoport, T.A. Vitamin K epoxide reductase prefers ER membrane-anchored thioredoxin-like redox partners. Proc. Natl. Acad. Sci. USA 107 (2010) 15027–15032. [PMID: 20696932]
[EC 1.17.4.4 created 1989 as EC 1.1.4.1, transferred 2014 to EC 1.17.4.4, modified 2018]
 
 
EC 1.17.5.1     
Accepted name: phenylacetyl-CoA dehydrogenase
Reaction: phenylacetyl-CoA + H2O + 2 quinone = phenylglyoxylyl-CoA + 2 quinol
For diagram of phenylacetyl-CoA metabolism, click here
Other name(s): phenylacetyl-CoA:acceptor oxidoreductase
Systematic name: phenylacetyl-CoA:quinone oxidoreductase
Comments: The enzyme from Thauera aromatica is a membrane-bound molybdenum—iron—sulfur protein. The enzyme is specific for phenylacetyl-CoA as substrate. Phenylacetate, acetyl-CoA, benzoyl-CoA, propanoyl-CoA, crotonyl-CoA, succinyl-CoA and 3-hydroxybenzoyl-CoA cannot act as substrates. The oxygen atom introduced into the product, phenylglyoxylyl-CoA, is derived from water and not molecular oxygen. Duroquinone, menaquinone and 2,6-dichlorophenolindophenol (DCPIP) can act as acceptor, but the likely physiological acceptor is ubiquinone [1]. A second enzyme, EC 3.1.2.25, phenylacetyl-CoA hydrolase, converts the phenylglyoxylyl-CoA formed into phenylglyoxylate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 210756-43-7
References:
1.  Rhee, S.K. and Fuchs, G. Phenylacetyl-CoA:acceptor oxidoreductase, a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 262 (1999) 507–515. [DOI] [PMID: 10336636]
2.  Schneider, S. and Fuchs, G. Phenylacetyl-CoA:acceptor oxidoreductase, a new α-oxidizing enzyme that produces phenylglyoxylate. Assay, membrane localization, and differential production in Thauera aromatica. Arch. Microbiol. 169 (1998) 509–516. [PMID: 9575237]
[EC 1.17.5.1 created 2004]
 
 
EC 1.17.5.3     
Accepted name: formate dehydrogenase-N
Reaction: formate + a quinone = CO2 + a quinol
Other name(s): Fdh-N; FdnGHI; nitrate-inducible formate dehydrogenase; formate dehydrogenase N; FDH-N; nitrate inducible Fdn; nitrate inducible formate dehydrogenase
Systematic name: formate:quinone oxidoreductase
Comments: The enzyme contains molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters and two heme b groups. Formate dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the menaquinone pool in the cytoplasmic membrane to a dissimilatory nitrate reductase (EC 1.7.5.1), which transfers electrons to nitrate in the cytoplasm. The system generates proton motive force under anaerobic conditions [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Enoch, H.G. and Lester, R.L. The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J. Biol. Chem. 250 (1975) 6693–6705. [PMID: 1099093]
2.  Jormakka, M., Tornroth, S., Byrne, B. and Iwata, S. Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science 295 (2002) 1863–1868. [DOI] [PMID: 11884747]
3.  Jormakka, M., Tornroth, S., Abramson, J., Byrne, B. and Iwata, S. Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 160–162. [PMID: 11752799]
[EC 1.17.5.3 created 2010 as EC 1.1.5.6, transferred 2017 to EC 1.17.5.3]
 
 
EC 1.21.98.1     
Accepted name: cyclic dehypoxanthinyl futalosine synthase
Reaction: dehypoxanthine futalosine + S-adenosyl-L-methionine = cyclic dehypoxanthinyl futalosine + 5′-deoxyadenosine + L-methionine
For diagram of the futalosine pathway, click here
Glossary: dehypoxanthine futalosine = 3-{3-[(2R,3S,4R)-3,4,5-trihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
cyclic dehypoxanthinyl futalosine = (2R,3S,4R)-3,4,5-trihydroxy-4′-oxo-3′,4,4′,5-tetrahydro-2’H,3H-spiro[furan-2,1′-naphthalene]-6′-carboxylate
Other name(s): MqnC; dehypoxanthinyl futalosine cyclase
Systematic name: dehypoxanthine futalosine:S-adenosyl-L-methionine oxidoreductase (cyclizing)
Comments: This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670–1673. [DOI] [PMID: 18801996]
2.  Cooper, L.E., Fedoseyenko, D., Abdelwahed, S.H., Kim, S.H., Dairi, T. and Begley, T.P. In vitro reconstitution of the radical S-adenosylmethionine enzyme MqnC involved in the biosynthesis of futalosine-derived menaquinone. Biochemistry 52 (2013) 4592–4594. [DOI] [PMID: 23763543]
[EC 1.21.98.1 created 2014 as EC 1.21.99.2, transferred 2014 to EC 1.21.98.1]
 
 
EC 1.21.99.2      
Transferred entry: EC 1.21.99.2, cyclic dehypoxanthinyl futalosine synthase. Now classified as EC 1.21.98.1, cyclic dehypoxanthinyl futalosine synthase.
[EC 1.21.99.2 created 2014, deleted 2014]
 
 
EC 1.21.99.5     
Accepted name: tetrachloroethene reductive dehalogenase
Reaction: trichloroethene + chloride + acceptor = tetrachloroethene + reduced acceptor
Glossary: methyl viologen = 1,1′-dimethyl-4,4′-bipyridine-1,1′-diium
Other name(s): tetrachloroethene reductase
Systematic name: acceptor:trichloroethene oxidoreductase (chlorinating)
Comments: This enzyme allows the common pollutant tetrachloroethene to support bacterial growth and is responsible for disposal of a number of chlorinated hydrocarbons. The reaction occurs in the reverse direction. The enzyme also reduces trichloroethene to dichloroethene. Although the physiological reductant is unknown, the supply of reductant in some organisms involves menaquinol, which is reduced by molecular hydrogen via the action of EC 1.12.5.1, hydrogen:quinone oxidoreductase. The enzyme contains a corrinoid and two iron-sulfur clusters. Methyl viologen can act as electron donor in vitro.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 163913-51-7
References:
1.  Holliger, C, Wohlfarth, G. and Diekert, G. Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev. 22 (1998) 383–398.
2.  Glod, G., Angst, W., Holliger, C. and Schwarzenbach, R.P. Corrinoid-mediated reduction of tetrachloroethene, trichloroethene, and trichlorofluoroethene in homogeneous aqueous solution: Reaction kinetics and reaction mechanisms. Environ. Sci. Technol. 31 (1997) 253–260.
3.  Neumann, A., Wohlfarth, G. and Diekert, G. Purification and characterization of tetrachloroethene reductive dehalogenase from Dehalospirillum multivorans. J. Biol. Chem. 271 (1996) 16515–16519. [DOI] [PMID: 8663199]
4.  Schumacher, W., Holliger, C., Zehnder, A.J.B. and Hagen, W.R. Redox chemistry of cobalamin and iron-sulfur cofactors in the tetrachloroethene reductase of Dehalobacter restrictus. FEBS Lett. 409 (1997) 421–425. [DOI] [PMID: 9224702]
5.  Schumacher, W. and Holliger, C. The proton/electron ratio of the menaquinone-dependent electron transport from dihydrogen to tetrachloroethene in "Dehalobacter restrictus". J. Bacteriol. 178 (1996) 2328–2333. [DOI] [PMID: 8636034]
[EC 1.21.99.5 created 2001 as EC 1.97.1.8, transferred 2017 to EC 1.21.99.5]
 
 
EC 1.97.1.8      
Transferred entry: tetrachloroethene reductive dehalogenase. Now EC 1.21.99.5, tetrachloroethene reductive dehalogenase
[EC 1.97.1.8 created 2001, deleted 2017]
 
 
EC 2.1.1.163     
Accepted name: demethylmenaquinone methyltransferase
Reaction: a demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + S-adenosyl-L-homocysteine
For diagram of vitamin-K biosynthesis, click here
Other name(s): S-adenosyl-L-methione—DMK methyltransferase; demethylmenaquinone C-methylase; 2-heptaprenyl-1,4-naphthoquinone methyltransferase; 2-demethylmenaquinone methyltransferase; S-adenosyl-L-methione:2-demethylmenaquinone methyltransferase
Systematic name: S-adenosyl-L-methione:demethylmenaquinone methyltransferase
Comments: The enzyme catalyses the last step in menaquinone biosynthesis. It is able to accept substrates with varying polyprenyl side chain length (the chain length is determined by polyprenyl diphosphate synthase)[1]. The enzyme from Escherichia coli also catalyses the conversion of 2-methoxy-6-octaprenyl-1,4-benzoquinone to 5-methoxy-2-methyl-3-octaprenyl-1,4-benzoquinone during the biosynthesis of ubiquinone [4]. The enzyme probably acts on menaquinol rather than menaquinone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Koike-Takeshita, A., Koyama, T. and Ogura, K. Identification of a novel gene cluster participating in menaquinone (vitamin K2) biosynthesis. Cloning and sequence determination of the 2-heptaprenyl-1,4-naphthoquinone methyltransferase gene of Bacillus stearothermophilus. J. Biol. Chem. 272 (1997) 12380–12383. [DOI] [PMID: 9139683]
2.  Wissenbach, U., Ternes, D. and Unden, G. An Escherichia coli mutant containing only demethylmenaquinone, but no menaquinone: effects on fumarate, dimethylsulfoxide, trimethylamine N-oxide and nitrate respiration. Arch. Microbiol. 158 (1992) 68–73. [PMID: 1444716]
3.  Catala, F., Azerad, R. and Lederer, E. Sur les propriétés de la desméthylménaquinone C-méthylase de Mycobacterium phlei. Int. Z. Vitaminforsch. 40 (1970) 363–373. [PMID: 5450997]
4.  Lee, P.T., Hsu, A.Y., Ha, H.T. and Clarke, C.F. A C-methyltransferase involved in both ubiquinone and menaquinone biosynthesis: isolation and identification of the Escherichia coli ubiE gene. J. Bacteriol. 179 (1997) 1748–1754. [DOI] [PMID: 9045837]
[EC 2.1.1.163 created 2009]
 
 
EC 2.1.1.201     
Accepted name: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase
Reaction: S-adenosyl-L-methionine + 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol = S-adenosyl-L-homocysteine + 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol
For diagram of ubiquinol biosynthesis, click here
Other name(s): ubiE (gene name, ambiguous)
Systematic name: S-adenosyl-L-methionine:2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol 5-C-methyltransferase
Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, when the COQ5 gene from Saccharomyces cerevisiae is introduced into Escherichia coli, it complements the respiratory deficiency of an ubiE mutant [3]. The bifunctional enzyme from Escherichia coli also catalyses the methylation of demethylmenaquinol-8 (this activity is classified as EC 2.1.1.163) [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lee, P.T., Hsu, A.Y., Ha, H.T. and Clarke, C.F. A C-methyltransferase involved in both ubiquinone and menaquinone biosynthesis: isolation and identification of the Escherichia coli ubiE gene. J. Bacteriol. 179 (1997) 1748–1754. [DOI] [PMID: 9045837]
2.  Young, I.G., McCann, L.M., Stroobant, P. and Gibson, F. Characterization and genetic analysis of mutant strains of Escherichia coli K-12 accumulating the biquinone precursors 2-octaprenyl-6-methoxy-1,4-benzoquinone and 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone. J. Bacteriol. 105 (1971) 769–778. [PMID: 4323297]
3.  Dibrov, E., Robinson, K.M. and Lemire, B.D. The COQ5 gene encodes a yeast mitochondrial protein necessary for ubiquinone biosynthesis and the assembly of the respiratory chain. J. Biol. Chem. 272 (1997) 9175–9181. [DOI] [PMID: 9083048]
4.  Barkovich, R.J., Shtanko, A., Shepherd, J.A., Lee, P.T., Myles, D.C., Tzagoloff, A. and Clarke, C.F. Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis. J. Biol. Chem. 272 (1997) 9182–9188. [DOI] [PMID: 9083049]
[EC 2.1.1.201 created 2011]
 
 
EC 2.1.1.350     
Accepted name: menaquinone C8-methyltransferase
Reaction: (1) 2 S-adenosyl-L-methionine + a menaquinone + reduced flavodoxin = S-adenosyl-L-homocysteine + L-methionine + 5′-deoxyadenosine + an 8-methylmenaquinone + oxidized flavodoxin
(2) 2 S-adenosyl-L-methionine + a 2-demethylmenaquinone + reduced flavodoxin = S-adenosyl-L-homocysteine + L-methionine + 5′-deoxyadenosine + a 2-demethyl-8-methylmenaquinone + oxidized flavodoxin
Other name(s): mqnK (gene name); menK (gene name)
Systematic name: S-adenosyl-L-methionine:menaquinone C8-methyltransferase
Comments: The enzyme, found in a wide range of bacteria and archaea, is a radical SAM (AdoMet) enzyme that utilizes two molecules of S-adenosyl-L-methionine, one as the methyl group donor, and one for the creation of a 5′-deoxyadenosine radical that drives the reaction forward.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hein, S., Klimmek, O., Polly, M., Kern, M. and Simon, J. A class C radical S-adenosylmethionine methyltransferase synthesizes 8-methylmenaquinone. Mol. Microbiol. 104 (2017) 449–462. [PMID: 28164386]
[EC 2.1.1.350 created 2018]
 
 
EC 2.2.1.9     
Accepted name: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
Reaction: isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2
Other name(s): SEPHCHC synthase; MenD
Systematic name: isochorismate:2-oxoglutarate 4-oxopentanoatetransferase (decarboxylating)
Comments: Requires Mg2+ for maximal activity. This enzyme is involved in the biosynthesis of vitamin K2 (menaquinone). In most anaerobes and all Gram-positive aerobes, menaquinone is the sole electron transporter in the respiratory chain and is essential for their survival. It had previously been thought that the products of the reaction were (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate (SHCHC), pyruvate and CO2 but it is now known that two separate enzymes are involved: this enzyme and EC 4.2.99.20, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. Under basic conditions, the product can spontaneously lose pyruvate to form SHCHC.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1112282-73-1
References:
1.  Jiang, M., Cao, Y., Guo, Z.F., Chen, M., Chen, X. and Guo, Z. Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry 46 (2007) 10979–10989. [DOI] [PMID: 17760421]
[EC 2.2.1.9 created 2008 (EC 2.5.1.64 created 2003, part-incorporated 2008)]
 
 
EC 2.5.1.30     
Accepted name: heptaprenyl diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): all-trans-heptaprenyl-diphosphate synthase; heptaprenyl pyrophosphate synthase; heptaprenyl pyrophosphate synthetase; HepPP synthase; HepPS; heptaprenylpyrophosphate synthetase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 4 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-heptaprenyl diphosphate, the isoprenoid side chain of ubiquinone-7 and menaquinone-7. The enzyme adds four isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 74506-59-5
References:
1.  Takahashi, I., Ogura, K. and Seto, S. Heptaprenyl pyrophosphate synthetase from Bacillus subtilis. J. Biol. Chem. 255 (1980) 4539–4543. [PMID: 6768722]
2.  Zhang, Y.W., Koyama, T., Marecak, D.M., Prestwich, G.D., Maki, Y. and Ogura, K. Two subunits of heptaprenyl diphosphate synthase of Bacillus subtilis form a catalytically active complex. Biochemistry 37 (1998) 13411–13420. [DOI] [PMID: 9748348]
3.  Zhang, Y.W., Li, X.Y., Sugawara, H. and Koyama, T. Site-directed mutagenesis of the conserved residues in component I of Bacillus subtilis heptaprenyl diphosphate synthase. Biochemistry 38 (1999) 14638–14643. [DOI] [PMID: 10545188]
4.  Suzuki, T., Zhang, Y.W., Koyama, T., Sasaki, D.Y. and Kurihara, K. Direct observation of substrate-enzyme complexation by surface forces measurement. J. Am. Chem. Soc. 128 (2006) 15209–15214. [DOI] [PMID: 17117872]
[EC 2.5.1.30 created 1984, modified 2010]
 
 
EC 2.5.1.64      
Transferred entry: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. The reaction that was attributed to this enzyme is now known to be catalysed by two separate enzymes: EC 2.2.1.9 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase) and EC 4.2.99.20 (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase)
[EC 2.5.1.64 created 2003, deleted 2008]
 
 
EC 2.5.1.74     
Accepted name: 1,4-dihydroxy-2-naphthoate polyprenyltransferase
Reaction: an all-trans-polyprenyl diphosphate + 1,4-dihydroxy-2-naphthoate = a demethylmenaquinone + diphosphate + CO2
For diagram of vitamin K biosynthesis, click here
Glossary: menaquinone = vitamin K2
Systematic name: all-trans-polyprenyl-diphosphate:1,4-dihydroxy-2-naphthoate polyprenyltransferase
Comments: This enzyme catalyses a step in the synthesis of menaquinone, in which the prenyl chain synthesized by polyprenyl diphosphate synthase is transferred to 1,4-dihydroxy-2-naphthoate (DHNA). The bacterial enzyme is an inner membrane protein [1], with the C-terminus located in the periplasm [3]. It is highly specific for DHNA but not for a specific length of the prenyl chain [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Shineberg, B. and Young, I.G. Biosynthesis of bacterial menaquinones: the membrane-associated 1,4-dihydroxy-2-naphthoate octaprenyltransferase of Escherichia coli. Biochemistry 15 (1976) 2754–2758. [PMID: 949474]
2.  Saito, Y. and Ogura, K. Biosynthesis of menaquinones. Enzymatic prenylation of 1,4-dihydroxy-2-naphthoate by Micrococcus luteus membrane fractions. J. Biochem. 89 (1981) 1445–1452. [PMID: 7275947]
3.  Suvarna, K., Stevenson, D., Meganathan, R. and Hudspeth, M.E. Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menA gene from Escherichia coli. J. Bacteriol. 180 (1998) 2782–2787. [PMID: 9573170]
4.  Daley, D.O., Rapp, M., Granseth, E., Melen, K., Drew, D. and von Heijne, G. Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 (2005) 1321–1323. [DOI] [PMID: 15919996]
[EC 2.5.1.74 created 2009]
 
 
EC 2.5.1.84     
Accepted name: all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific]
Reaction: geranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-nonaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: solanesyl diphosphate = all-trans-nonaprenyl diphosphate
Other name(s): nonaprenyl diphosphate synthase (ambiguous); solanesyl diphosphate synthase (ambiguous); SolPP synthase (ambiguous); SPP-synthase (ambiguous); SPP synthase (ambiguous); solanesyl-diphosphate synthase (ambiguous); OsSPS2
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 7 isopentenyl units)
Comments: (2E,6E)-Farnesyl diphosphate and geranylgeranyl diphosphate are less effective as substrates than geranyl diphosphate. The enzyme is involved in the synthesis of the side chain of menaquinone-9 [1]. In Oryza sativa the enzyme SPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sagami, H., Ogura, K. and Seto, S. Solanesyl pyrophosphate synthetase from Micrococcus lysodeikticus. Biochemistry 16 (1977) 4616–4622. [PMID: 911777]
2.  Fujii, H., Sagami, H., Koyama, T., Ogura, K., Seto, S., Baba, T. and Allen, C.M. Variable product specificity of solanesyl pyrophosphate synthetase. Biochem. Biophys. Res. Commun. 96 (1980) 1648–1653. [DOI] [PMID: 7447947]
3.  Ohara, K., Sasaki, K. and Yazaki, K. Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa. J. Exp. Bot. 61 (2010) 2683–2692. [DOI] [PMID: 20421194]
4.  Ohnuma, S., Koyama, T. and Ogura, K. Purification of solanesyl-diphosphate synthase from Micrococcus luteus. A new class of prenyltransferase. J. Biol. Chem. 266 (1991) 23706–23713. [PMID: 1748647]
5.  Gotoh, T., Koyama, T. and Ogura, K. Farnesyl diphosphate synthase and solanesyl diphosphate synthase reactions of diphosphate-modified allylic analogs: the significance of the diphosphate linkage involved in the allylic substrates for prenyltransferase. J. Biochem. 112 (1992) 20–27. [PMID: 1429508]
6.  Teclebrhan, H., Olsson, J., Swiezewska, E. and Dallner, G. Biosynthesis of the side chain of ubiquinone:trans-prenyltransferase in rat liver microsomes. J. Biol. Chem. 268 (1993) 23081–23086. [PMID: 8226825]
[EC 2.5.1.84 created 1972 as EC 2.5.1.11, part transferred 2010 to EC 2.5.1.84]
 
 
EC 2.5.1.90     
Accepted name: all-trans-octaprenyl-diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-octaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Glossary: all-trans-octaprenyl diphosphate = OPP
Other name(s): octaprenyl-diphosphate synthase; octaprenyl pyrophosphate synthetase; polyprenylpyrophosphate synthetase; terpenoidallyltransferase; terpenyl pyrophosphate synthetase; trans-heptaprenyltranstransferase; trans-prenyltransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 5 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-octaprenyl diphosphate, the isoprenoid side chain of ubiquinone-8 and menaquinone-8. The enzyme adds five isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fujisaki, S., Nishino, T. and Katsuki, H. Isoprenoid synthesis in Escherichia coli. Separation and partial purification of four enzymes involved in the synthesis. J. Biochem. 99 (1986) 1327–1337. [PMID: 3519603]
2.  Asai, K., Fujisaki, S., Nishimura, Y., Nishino, T., Okada, K., Nakagawa, T., Kawamukai, M. and Matsuda, H. The identification of Escherichia coli ispB (cel) gene encoding the octaprenyl diphosphate synthase. Biochem. Biophys. Res. Commun. 202 (1994) 340–345. [DOI] [PMID: 8037730]
[EC 2.5.1.90 created 2010]
 
 
EC 2.5.1.91     
Accepted name: all-trans-decaprenyl-diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-decaprenyl diphosphate
For diagram of terpenoid biosynthesis, click here
Other name(s): decaprenyl-diphosphate synthase; decaprenyl pyrophosphate synthetase; polyprenylpyrophosphate synthetase; terpenoidallyltransferase; terpenyl pyrophosphate synthetase; trans-prenyltransferase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 7 isopentenyl units)
Comments: This enzyme catalyses the condensation reactions resulting in the formation of all-trans-decaprenyl diphosphate, the isoprenoid side chain of ubiquinone-10 and menaquinone-10. The enzyme adds seven isopentenyl diphosphate molecules sequentially to farnesyl diphosphate with trans stereochemistry.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Saiki, R., Nagata, A., Kainou, T., Matsuda, H. and Kawamukai, M. Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans. FEBS J. 272 (2005) 5606–5622. [DOI] [PMID: 16262699]
[EC 2.5.1.91 created 2010]
 
 
EC 2.5.1.120     
Accepted name: aminodeoxyfutalosine synthase
Reaction: S-adenosyl-L-methionine + 3-[(1-carboxyvinyl)oxy]benzoate + H2O = 6-amino-6-deoxyfutalosine + L-methionine + HCO3-
For diagram of the futalosine pathway, click here
Glossary: 6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
Other name(s): MqnE; AFL synthase; aminofutalosine synthase; S-adenosyl-L-methionine:3-[(1-carboxyvinyl)-oxy]benzoate adenosyltransferase (bicarbonate-hydrolysing, 6-amino-6-deoxyfutalosine-forming)
Systematic name: S-adenosyl-L-methionine:3-[(1-carboxyvinyl)-oxy]benzoate adenosyltransferase (HCO3--hydrolysing, 6-amino-6-deoxyfutalosine-forming)
Comments: This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. S-Adenosyl-L-methionine acts as both a radical generator and as the source of the transferred adenosyl group. The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318–15321. [DOI] [PMID: 24083939]
[EC 2.5.1.120 created 2014]
 
 
EC 2.8.2.40     
Accepted name: ω-hydroxy-β-dihydromenaquinone-9 sulfotransferase
Reaction: 3′-phosphoadenylyl sulfate + ω-hydroxy-β-dihydromenaquinone-9 = adenosine 3′,5′-bisphosphate + ω-sulfo-β-dihydromenaquinone-9
Glossary: β-dihydromenaquinone-9 = MK-9(II-H2) = 2-methyl-3-[(2E,10E,14E,18E,22E,26E,30E,33E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,10,14,18,22,26,30,33-octaen-1-yl]naphthalene-1,4-dione
Other name(s): stf3 (gene name)
Systematic name: 3′-phosphoadenylyl-sulfate:ω-hydroxy-β-dihydromenaquinone-9 sulfotransferase
Comments: The enzyme catalyses the last step in the production of ω-sulfo-β-dihydromenaquinone-9 by members of the Mycobacterium tuberculosis complex.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mougous, J.D., Senaratne, R.H., Petzold, C.J., Jain, M., Lee, D.H., Schelle, M.W., Leavell, M.D., Cox, J.S., Leary, J.A., Riley, L.W. and Bertozzi, C.R. A sulfated metabolite produced by stf3 negatively regulates the virulence of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103 (2006) 4258–4263. [PMID: 16537518]
2.  Holsclaw, C.M., Sogi, K.M., Gilmore, S.A., Schelle, M.W., Leavell, M.D., Bertozzi, C.R. and Leary, J.A. Structural characterization of a novel sulfated menaquinone produced by stf3 from Mycobacterium tuberculosis. ACS Chem. Biol. 3 (2008) 619–624. [PMID: 18928249]
[EC 2.8.2.40 created 2021]
 
 
EC 3.1.2.28     
Accepted name: 1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Reaction: 1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA
For diagram of vitamin K biosynthesis, click here
Other name(s): menI (gene name); ydiL (gene name)
Systematic name: 1,4-dihydroxy-2-naphthoyl-CoA hydrolase
Comments: This enzyme participates in the synthesis of menaquinones [4], phylloquinone [3], as well as several plant pigments [1,2]. The enzyme from the cyanobacterium Synechocystis sp. PCC 6803 does not accept benzoyl-CoA or phenylacetyl-CoA as substrates [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Muller, W. and Leistner, E. 1,4-Naphthoquinone, an intermediate in juglone (5-hydroxy-1,4-naphthoquinone) biosynthesis. Phytochemistry 15 (1976) 407–410.
2.  Eichinger, D., Bacher, A., Zenk, M.H. and Eisenreich, W. Quantitative assessment of metabolic flux by 13C NMR analysis. Biosynthesis of anthraquinones in Rubia tinctorum. J. Am. Chem. Soc. 121 (1999) 7469–7475.
3.  Widhalm, J.R., van Oostende, C., Furt, F. and Basset, G.J. A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1. Proc. Natl. Acad. Sci. USA 106 (2009) 5599–5603. [DOI] [PMID: 19321747]
4.  Chen, M., Ma, X., Chen, X., Jiang, M., Song, H. and Guo, Z. Identification of a hotdog fold thioesterase involved in the biosynthesis of menaquinone in Escherichia coli. J. Bacteriol. 195 (2013) 2768–2775. [DOI] [PMID: 23564174]
[EC 3.1.2.28 created 2010]
 
 
EC 3.2.2.26     
Accepted name: futalosine hydrolase
Reaction: futalosine + H2O = dehypoxanthine futalosine + hypoxanthine
For diagram of the futalosine pathway, click here
Glossary: futalosine = 3-(3-((3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9(6H)-yl)tetrahydrofuran-2-yl)propanoyl)benzoate
dehypoxanthine futalosine = 7-(3-carboxyphenyl)-D-ribo-7-dehydro-5,6-dideoxyheptose
Other name(s): futalosine nucleosidase; MqnB (ambiguous)
Systematic name: futalosine ribohydrolase
Comments: This enzyme, which is specific for futalosine, catalyses the second step of a novel menaquinone biosynthetic pathway that is found in some prokaryotes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670–1673. [DOI] [PMID: 18801996]
[EC 3.2.2.26 created 2008]
 
 
EC 3.2.2.30     
Accepted name: aminodeoxyfutalosine nucleosidase
Reaction: 6-amino-6-deoxyfutalosine + H2O = dehypoxanthine futalosine + adenine
For diagram of the futalosine pathway, click here
Glossary: 6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
dehypoxanthine futalosine = 3-{3-[(2R,3S,4R)-3,4,5-trihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
Other name(s): AFL nucleosidase; aminofutalosine nucleosidase; methylthioadenosine nucleosidase; MqnB (ambiguous)
Systematic name: 6-amino-6-deoxyfutalosine ribohydrolase
Comments: The enzyme, found in several bacterial species, catalyses a step in a modified futalosine pathway for menaquinone biosynthesis. While the enzyme from some organisms also has the activity of EC 3.2.2.9, adenosylhomocysteine nucleosidase, the enzyme from Chlamydia trachomatis is specific for 6-amino-6-deoxyfutalosine [7].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670–1673. [DOI] [PMID: 18801996]
2.  Li, X., Apel, D., Gaynor, E.C. and Tanner, M.E. 5′-methylthioadenosine nucleosidase is implicated in playing a key role in a modified futalosine pathway for menaquinone biosynthesis in Campylobacter jejuni. J. Biol. Chem. 286 (2011) 19392–19398. [DOI] [PMID: 21489995]
3.  Arakawa, C., Kuratsu, M., Furihata, K., Hiratsuka, T., Itoh, N., Seto, H. and Dairi, T. Diversity of the early step of the futalosine pathway. Antimicrob. Agents Chemother. 55 (2011) 913–916. [DOI] [PMID: 21098241]
4.  Wang, S., Haapalainen, A.M., Yan, F., Du, Q., Tyler, P.C., Evans, G.B., Rinaldo-Matthis, A., Brown, R.L., Norris, G.E., Almo, S.C. and Schramm, V.L. A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori. Biochemistry 51 (2012) 6892–6894. [DOI] [PMID: 22891633]
5.  Mishra, V. and Ronning, D.R. Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5′-alkylthio binding subsite. Biochemistry 51 (2012) 9763–9772. [DOI] [PMID: 23148563]
6.  Kim, R.Q., Offen, W.A., Davies, G.J. and Stubbs, K.A. Structural enzymology of Helicobacter pylori methylthioadenosine nucleosidase in the futalosine pathway. Acta Crystallogr. D Biol. Crystallogr. 70 (2014) 177–185. [DOI] [PMID: 24419390]
7.  Barta, M.L., Thomas, K., Yuan, H., Lovell, S., Battaile, K.P., Schramm, V.L. and Hefty, P.S. Structural and biochemical characterization of Chlamydia trachomatis hypothetical protein CT263 supports that menaquinone synthesis occurs through the futalosine pathway. J. Biol. Chem. 289 (2014) 32214–32229. [DOI] [PMID: 25253688]
[EC 3.2.2.30 created 2014]
 
 
EC 3.5.4.40     
Accepted name: aminodeoxyfutalosine deaminase
Reaction: 6-amino-6-deoxyfutalosine + H2O = futalosine + NH3
For diagram of the futalosine pathway, click here
Glossary: 6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
futalosine = 3-{3-[(3S,4R)-3,4-dihydroxy-5-(6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-2-yl]propanoyl}benzoate
Other name(s): AFL deaminase; aminofutalosine deaminase; mqnX (gene name)
Systematic name: 6-amino-6-deoxyfutalosine deaminase
Comments: The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Arakawa, C., Kuratsu, M., Furihata, K., Hiratsuka, T., Itoh, N., Seto, H. and Dairi, T. Diversity of the early step of the futalosine pathway. Antimicrob. Agents Chemother. 55 (2011) 913–916. [DOI] [PMID: 21098241]
2.  Goble, A.M., Toro, R., Li, X., Ornelas, A., Fan, H., Eswaramoorthy, S., Patskovsky, Y., Hillerich, B., Seidel, R., Sali, A., Shoichet, B.K., Almo, S.C., Swaminathan, S., Tanner, M.E. and Raushel, F.M. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry 52 (2013) 6525–6536. [DOI] [PMID: 23972005]
[EC 3.5.4.40 created 2014]
 
 
EC 4.1.3.36     
Accepted name: 1,4-dihydroxy-2-naphthoyl-CoA synthase
Reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
For diagram of vitamin-K biosynthesis, click here
Other name(s): naphthoate synthase; 1,4-dihydroxy-2-naphthoate synthase; dihydroxynaphthoate synthase; o-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing); MenB; o-succinylbenzoyl-CoA dehydratase (cyclizing)
Systematic name: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA dehydratase (cyclizing)
Comments: This enzyme is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by EC 3.1.2.28, 1,4-dihydroxy-2-naphthoyl-CoA hydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61328-42-5
References:
1.  Meganathan, R. and Bentley, R. Menaquinone (vitamin K2) biosynthesis: conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid by Mycobacterium phlei enzymes. J. Bacteriol. 140 (1979) 92–98. [PMID: 500558]
2.  Kolkmann, R. and Leistner, E. 4-(2′-Carboxyphenyl)-4-oxobutyryl coenzyme A ester, an intermediate in vitamin K2 (menaquinone) biosynthesis. Z. Naturforsch. C: Sci. 42 (1987) 1207–1214. [PMID: 2966501]
3.  Johnson, T.W., Shen, G., Zybailov, B., Kolling, D., Reategui, R., Beauparlant, S., Vassiliev, I.R., Bryant, D.A., Jones, A.D., Golbeck, J.H. and Chitnis, P.R. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. PCC 6803. J. Biol. Chem. 275 (2000) 8523–8530. [DOI] [PMID: 10722690]
4.  Truglio, J.J., Theis, K., Feng, Y., Gajda, R., Machutta, C., Tonge, P.J. and Kisker, C. Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. J. Biol. Chem. 278 (2003) 42352–42360. [DOI] [PMID: 12909628]
[EC 4.1.3.36 created 1992, modified 2010]
 
 
EC 4.2.1.113     
Accepted name: o-succinylbenzoate synthase
Reaction: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O
For diagram of vitamin K biosynthesis, click here
Glossary: 2-succinylbenzoate = o-succinylbenzoate = 4-(2-carboxyphenyl)-4-oxobutanoate
Other name(s): o-succinylbenzoic acid synthase; OSB synthase; OSBS; 2-succinylbenzoate synthase; MenC
Systematic name: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydro-lyase (2-succinylbenzoate-forming)
Comments: Belongs to the enolase superfamily and requires divalent cations, preferably Mg2+ or Mn2+, for activity. Forms part of the vitamin-K-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 97089-83-3
References:
1.  Sharma, V., Meganathan, R. and Hudspeth, M.E. Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli. J. Bacteriol. 175 (1993) 4917–4921. [DOI] [PMID: 8335646]
2.  Klenchin, V.A., Taylor Ringia, E.A., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli. Biochemistry 42 (2003) 14427–14433. [DOI] [PMID: 14661953]
3.  Palmer, D.R., Garrett, J.B., Sharma, V., Meganathan, R., Babbitt, P.C. and Gerlt, J.A. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry 38 (1999) 4252–4258. [DOI] [PMID: 10194342]
4.  Thompson, T.B., Garrett, J.B., Taylor, E.A., Meganathan, R., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate. Biochemistry 39 (2000) 10662–10676. [DOI] [PMID: 10978150]
5.  Taylor Ringia, E.A., Garrett, J.B., Thoden, J.B., Holden, H.M., Rayment, I. and Gerlt, J.A. Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry 43 (2004) 224–229. [DOI] [PMID: 14705949]
[EC 4.2.1.113 created 2007]
 
 
EC 4.2.1.151     
Accepted name: chorismate dehydratase
Reaction: chorismate = 3-[(1-carboxyvinyl)oxy]benzoate + H2O
For diagram of the futalosine pathway, click here
Other name(s): MqnA
Systematic name: chorismate hydro-lyase (3-[(1-carboxyvinyl)oxy]benzoate-forming)
Comments: The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318–15321. [DOI] [PMID: 24083939]
[EC 4.2.1.151 created 2014]
 
 
EC 4.2.99.20     
Accepted name: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
Reaction: 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate + pyruvate
For diagram of reaction, click here and for diagram of vitamin K biosynthesis, click here
Other name(s): 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase; 6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate synthase; SHCHC synthase; MenH; YfbB
Systematic name: 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate pyruvate-lyase [(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate-forming]
Comments: This enzyme is involved in the biosynthesis of vitamin K2 (menaquinone). In most anaerobes and all Gram-positive aerobes, menaquinone is the sole electron transporter in the respiratory chain and is essential for their survival. It had previously been thought that the reactions carried out by this enzyme and EC 2.2.1.9, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase, were carried out by a single enzyme but this has since been disproved [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 122007-88-9
References:
1.  Jiang, M., Chen, X., Guo, Z.F., Cao, Y., Chen, M. and Guo, Z. Identification and characterization of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase in the menaquinone biosynthesis of Escherichia coli. Biochemistry 47 (2008) 3426–3434. [DOI] [PMID: 18284213]
2.  Jiang, M., Cao, Y., Guo, Z.F., Chen, M., Chen, X. and Guo, Z. Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry 46 (2007) 10979–10989. [DOI] [PMID: 17760421]
[EC 4.2.99.20 created 2008 (EC 2.5.1.64 created 2003, part-incorporated 2008)]
 
 
EC 5.4.4.2     
Accepted name: isochorismate synthase
Reaction: chorismate = isochorismate
For diagram of shikimate and chorismate biosynthesis, click here
Other name(s): MenF
Systematic name: isochorismate hydroxymutase
Comments: Requires Mg2+. The reaction is reversible.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37318-53-9
References:
1.  Young, I.G. and Gibson, F. Regulation of the enzymes involved in the biosynthesis of 2,3-dihydroxybenzoic acid in Aerobacter aerogenes and Escherichia coli. Biochim. Biophys. Acta 177 (1969) 401–411. [DOI] [PMID: 4306838]
2.  van Tegelen, L.J., Moreno, P.R., Croes, A.F., Verpoorte, R. and Wullems, G.J. Purification and cDNA cloning of isochorismate synthase from elicited cell cultures of Catharanthus roseus. Plant Physiol. 119 (1999) 705–712. [PMID: 9952467]
3.  Dahm, C., Müller, R., Schulte, G., Schmidt, K. and Leistner, E. The role of isochorismate hydroxymutase genes entC and menF in enterobactin and menaquinone biosynthesis in Escherichia coli. Biochim. Biophys. Acta 1425 (1998) 377–386. [DOI] [PMID: 9795253]
4.  Daruwala, R., Kwon, O., Meganathan, R. and Hudspeth, M.E. A new isochorismate synthase specifically involved in menaquinone (vitamin K2) biosynthesis encoded by the menF gene. FEMS Microbiol. Lett. 140 (1996) 159–163. [PMID: 8764478]
[EC 5.4.4.2 created 1972 as EC 5.4.99.6, transferred 2003 to EC 5.4.4.2]
 
 
EC 6.2.1.26     
Accepted name: o-succinylbenzoate—CoA ligase
Reaction: ATP + 2-succinylbenzoate + CoA = AMP + diphosphate + 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA
For diagram of vitamin K biosynthesis, click here
Glossary: 2-succinylbenzoate = o-succinylbenzoate = 4-(2-carboxyphenyl)-4-oxobutanoate
Other name(s): o-succinylbenzoyl-coenzyme A synthetase; o-succinylbenzoate:CoA ligase (AMP-forming)
Systematic name: 2-succinylbenzoate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 72506-70-8
References:
1.  Heide, L., Arendt, S. and Leistner, E. Enzymatic-synthesis, characterization, and metabolism of the coenzyme-A ester of o-succinylbenzoic acid, an intermediate in menaquinone (vitamin K2) biosynthesis. J. Biol. Chem. 257 (1982) 7396–7400. [PMID: 7045104]
2.  Kolkmann, R. and Leistner, E. 4-(2′-Carboxyphenyl)-4-oxobutyryl coenzyme A ester, an intermediate in vitamin K2 (menaquinone) biosynthesis. Z. Naturforsch. C: Sci. 42 (1987) 1207–1214. [PMID: 2966501]
3.  Meganathan, R. and Bentley, R. Menaquinone (vitamin K2) biosynthesis: conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid by Mycobacterium phlei enzymes. J. Bacteriol. 140 (1979) 92–98. [PMID: 500558]
[EC 6.2.1.26 created 1992]
 
 
EC 7.1.1.5     
Accepted name: menaquinol oxidase (H+-transporting)
Reaction: 2 menaquinol + O2 + n H+[side 1] = 2 menaquinone + 2 H2O + n H+[side 2]
Other name(s): cytochrome aa3-600 oxidase; cytochrome bd oxidase; menaquinol:O2 oxidoreductase (H+-transporting)
Systematic name: menaquinol:oxygen oxidoreductase (H+-transporting)
Comments: Cytochrome aa3-600, one of the principal respiratory oxidases from Bacillus subtilis, is a member of the heme-copper superfamily of oxygen reductases, and is a close homologue of the cytochrome bo3 ubiquinol oxidase from Escherichia coli, but uses menaquinol instead of ubiquinol as a substrate.The enzyme also pumps protons across the membrane bilayer, generating a proton motive force.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lauraeus, M. and Wikstrom, M. The terminal quinol oxidases of Bacillus subtilis have different energy conservation properties. J. Biol. Chem. 268 (1993) 11470–11473. [PMID: 8388393]
2.  Lemma, E., Simon, J., Schagger, H. and Kroger, A. Properties of the menaquinol oxidase (Qox) and of qox deletion mutants of Bacillus subtilis. Arch. Microbiol. 163 (1995) 432–438. [PMID: 7575098]
3.  Yi, S.M., Narasimhulu, K.V., Samoilova, R.I., Gennis, R.B. and Dikanov, S.A. Characterization of the semiquinone radical stabilized by the cytochrome aa3-600 menaquinol oxidase of Bacillus subtilis. J. Biol. Chem. 285 (2010) 18241–18251. [DOI] [PMID: 20351111]
[EC 7.1.1.5 created 2011 as EC 1.10.3.12, transferred 2018 to EC 7.1.1.5]
 
 
EC 7.1.1.8     
Accepted name: quinol—cytochrome-c reductase
Reaction: quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H+[side 2]
Other name(s): ubiquinol—cytochrome-c reductase; coenzyme Q-cytochrome c reductase; dihydrocoenzyme Q-cytochrome c reductase; reduced ubiquinone-cytochrome c reductase; complex III (mitochondrial electron transport); ubiquinone-cytochrome c reductase; ubiquinol-cytochrome c oxidoreductase; reduced coenzyme Q-cytochrome c reductase; ubiquinone-cytochrome c oxidoreductase; reduced ubiquinone-cytochrome c oxidoreductase; mitochondrial electron transport complex III; ubiquinol-cytochrome c-2 oxidoreductase; ubiquinone-cytochrome b-c1 oxidoreductase; ubiquinol-cytochrome c2 reductase; ubiquinol-cytochrome c1 oxidoreductase; CoQH2-cytochrome c oxidoreductase; ubihydroquinol:cytochrome c oxidoreductase; coenzyme QH2-cytochrome c reductase; QH2:cytochrome c oxidoreductase; ubiquinol:ferricytochrome-c oxidoreductase
Systematic name: quinol:ferricytochrome-c oxidoreductase
Comments: The enzyme, often referred to as the cytochrome bc1 complex or complex III, is the third complex in the electron transport chain. It is present in the mitochondria of all aerobic eukaryotes and in the inner membranes of most bacteria. The mammalian enzyme contains cytochromes b-562, b-566 and c1, and a 2-iron ferredoxin. Depending on the organism and physiological conditions, the enzyme extrudes either two or four protons from the cytoplasmic to the non-cytoplasmic compartment (cf. EC 1.6.99.3, NADH dehydrogenase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-03-6
References:
1.  Marres, C.A.M. and Slater, E.C. Polypeptide composition of purified QH2:cytochrome c oxidoreductase from beef-heart mitochondria. Biochim. Biophys. Acta 462 (1977) 531–548. [DOI] [PMID: 597492]
2.  Rieske, J.S. Composition, structure, and function of complex III of the respiratory chain. Biochim. Biophys. Acta 456 (1976) 195–247. [PMID: 788795]
3.  Wikström, M., Krab, K. and Saraste, M. Proton-translocating cytochrome complexes. Annu. Rev. Biochem. 50 (1981) 623–655. [DOI] [PMID: 6267990]
4.  Sone, N., Tsuchiya, N., Inoue, M. and Noguchi, S. Bacillus stearothermophilus qcr operon encoding rieske FeS protein, cytochrome b6, and a novel-type cytochrome c1 of quinol-cytochrome c reductase. J. Biol. Chem. 271 (1996) 12457–12462. [DOI] [PMID: 8647852]
5.  Yu, J. and Le Brun, N.E. Studies of the cytochrome subunits of menaquinone:cytochrome c reductase (bc complex) of Bacillus subtilis. Evidence for the covalent attachment of heme to the cytochrome b subunit. J. Biol. Chem. 273 (1998) 8860–8866. [DOI] [PMID: 9535866]
6.  Elbehti, A., Nitschke, W., Tron, P., Michel, C. and Lemesle-Meunier, D. Redox components of cytochrome bc-type enzymes in acidophilic prokaryotes. I. Characterization of the cytochrome bc1-type complex of the acidophilic ferrous ion-oxidizing bacterium Thiobacillus ferrooxidans. J. Biol. Chem. 274 (1999) 16760–16765. [DOI] [PMID: 10358017]
[EC 7.1.1.8 created 1978 as EC 1.10.2.2, modified 2013, transferred 2018 to EC 7.1.1.8]
 
 


Data © 2001–2022 IUBMB
Web site © 2005–2022 Andrew McDonald