The Enzyme Database

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EC 2.5.1.6     
Accepted name: methionine adenosyltransferase
Reaction: ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl-L-methionine
For diagram of reaction, click here
Other name(s): adenosylmethionine synthetase; ATP-methionine adenosyltransferase; methionine S-adenosyltransferase; methionine-activating enzyme; S-adenosyl-L-methionine synthetase; S-adenosylmethionine synthase; S-adenosylmethionine synthetase; AdoMet synthetase
Systematic name: ATP:L-methionine S-adenosyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9012-52-6
References:
1.  Cantoni, G.L. S-Adenosylmethionine: A new intermediate formed enzymatically from L-methionine and adenosinetriphosphate. J. Biol. Chem. 204 (1953) 403–416. [PMID: 13084611]
2.  Cantoni, G.L. and Durell, J. Activation of methionine for transmethylation. II. The methionine-activating enzyme: studies on the mechanism of reaction. J. Biol. Chem. 225 (1957) 1033–1048. [PMID: 13416303]
3.  Mudd, S.H. and Cantoni, G.L. Activation of methionine for transmethylation. III. The methionine-activating enzyme of bakers' yeast. J. Biol. Chem. 231 (1958) 481–492. [PMID: 13538985]
[EC 2.5.1.6 created 1961 as EC 2.4.2.13, transferred 1965 to EC 2.5.1.6]
 
 
EC 2.5.1.60     
Accepted name: protein geranylgeranyltransferase type II
Reaction: geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl-protein + diphosphate
Other name(s): GGTaseII; Rab geranylgeranyltransferase; RabGGTase; geranylgeranyl-diphosphate,geranylgeranyl-diphosphate:protein-cysteine geranyltransferase
Systematic name: geranylgeranyl-diphosphate:protein-cysteine geranyltransferase
Comments: This enzyme, along with protein farnesyltransferase (EC 2.5.1.58) and protein geranylgeranyltransferase type I (EC 2.5.1.59), constitutes the protein prenyltransferase family of enzymes. Attaches geranylgeranyl groups to two C-terminal cysteines in Ras-related GTPases of a single family, the Rab family (Ypt/Sec4 in lower eukaryotes) that terminate in XXCC, XCXC and CCXX motifs. Reaction is entirely dependent on the Rab substrate being bound to Rab escort protein (REP). Post-translational modification with the geranylgeranyl moiety is essential for Rab GTPases to be able to control the processes of membrane docking and fusion [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 135371-29-8
References:
1.  Casey, P.J. and Seabra, M.C. Protein prenyltransferases. J. Biol. Chem. 271 (1996) 5289–5292. [DOI] [PMID: 8621375]
2.  Wilson, A.L., Erdman, R.A., Castellano, F. and Maltese, W.A. Prenylation of Rab8 GTPase by type I and type II geranylgeranyl transferases. Biochem. J. 333 (1998) 497–504. [PMID: 9677305]
3.  Zhang, H., Seabra, M.C. and Deisenhofer, J. Crystal structure of Rab geranylgeranyltransferase at 2.0 Å resolution. Structure 8 (2000) 241–251. [PMID: 10745007]
4.  Thomä, N.H., Niculae, A., Goody, R.S. and Alexandrov, K. Double prenylation by RabGGTase can proceed without dissociation of the mono-prenylated intermediate. J. Biol. Chem. 276 (2001) 48631–48636. [DOI] [PMID: 11591706]
5.  Rak, A., Niculae, A., Kalinin, A., Thomä, N.H., Sidorovitch, V., Goody, R.S. and Alexandrov, K. In vitro assembly, purification, and crystallization of the Rab geranylgeranyl transferase:substrate complex. Protein Expr. Purif. 25 (2002) 23–30. [DOI] [PMID: 12071695]
6.  Gibbs, R.A. Prenyl transfer and the enzymes of terpenoid and steroid biosynthesis. In: Sinnott, M. (Ed.), Comprehensive Biological Catalysis. A Mechanistic Reference, vol. 1, Academic Press, San Diego, CA, 1998, pp. 31–118.
[EC 2.5.1.60 created 2003]
 
 
EC 2.5.1.61     
Accepted name: hydroxymethylbilane synthase
Reaction: 4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3
For diagram of the early stages of porphyrin biosynthesis, click here
Other name(s): HMB-synthase; porphobilinogen deaminase; pre-uroporphyrinogen synthase; uroporphyrinogen I synthase; uroporphyrinogen I synthetase; uroporphyrinogen synthase; uroporphyrinogen synthetase; porphobilinogen ammonia-lyase (polymerizing); (4-[2-carboxyethyl]-3-[carboxymethyl]pyrrol-2-yl)methyltransferase (hydrolysing)
Systematic name: porphobilinogen:(4-[2-carboxyethyl]-3-[carboxymethyl]pyrrol-2-yl)methyltransferase (hydrolysing)
Comments: The enzyme works by stepwise addition of pyrrolylmethyl groups until a hexapyrrole is present at the active centre. The terminal tetrapyrrole is then hydrolysed to yield the product, leaving a cysteine-bound dipyrrole on which assembly continues. In the presence of a second enzyme, EC 4.2.1.75 uroporphyrinogen-III synthase, which is often called cosynthase, the product is cyclized to form uroporphyrinogen-III. If EC 4.2.1.75 is absent, the hydroxymethylbilane cyclizes spontaneously to form uroporphyrinogen I.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9074-91-3
References:
1.  Battersby, A.R., Fookes, C.J.R., Matcham, G.W.J. and McDonald, E. Biosynthesis of the pigments of life: formation of the macrocycle. Nature 285 (1980) 17–21. [PMID: 6769048]
2.  Frydman, R.B. and Feinstein, G. Studies on porphobilinogen deaminase and uroporphyrinogen 3 cosynthase from human erythrocytes. Biochim. Biophys. Acta 350 (1974) 358–373. [DOI] [PMID: 4847568]
3.  Levin, E.Y. and Coleman, D.L. The enzymatic conversion of porphobilinogen to uroporphyrinogen catalyzed by extracts of hematopoietic mouse spleen. J. Biol. Chem. 242 (1967) 4247–4253. [PMID: 6061709]
4.  Warren, M.J. and Jordan, P.M. Investigation into the nature of substrate binding to the dipyrromethane cofactor of Escherichia coli porphobilinogen deaminase. Biochemistry 27 (1988) 9020–9030. [PMID: 3069132]
5.  Miller, A.D., Hart, G.J., Packman, L.C. and Battersby, A.R. Evidence that the pyrromethane cofactor of hydroxymethylbilane synthase (porphobilinogen deaminase) is bound to the protein through the sulphur atom of cysteine-242. Biochem. J. 254 (1988) 915–918. [PMID: 3196304]
6.  Battersby, A.R. Tetrapyrroles: the pigments of life. Nat. Prod. Rep. 17 (2000) 507–526. [PMID: 11152419]
[EC 2.5.1.61 created 1972 as EC 4.3.1.8, transferred 2003 to EC 2.6.1.61]
 
 
EC 2.5.1.62     
Accepted name: chlorophyll synthase
Reaction: chlorophyllide a + phytyl diphosphate = chlorophyll a + diphosphate
For diagram of the later stages of chlorophyll biosynthesis, click here
Systematic name: chlorophyllide-a:phytyl-diphosphate phytyltransferase
Comments: Requires Mg2+. The enzyme is modified by binding of the first substrate, phytyl diphosphate, before reaction of the modified enzyme with the second substrate, chlorophyllide a, can occur. The reaction also occurs when phytyl diphosphate is replaced by geranylgeranyl diphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9077-08-1
References:
1.  Schmid, H.C., Rassadina, V., Oster, U., Schoch, S. and Rüdiger, W. Pre-loading of chlorophyll synthase with tetraprenyl diphosphate is an obligatory step in chlorophyll biosynthesis. Biol. Chem. 383 (2002) 1769–1778. [DOI] [PMID: 12530542]
2.  Oster, U., Bauer, C.E. and Rüdiger, W. Characterization of chlorophyll a and bacteriochlorophyll a synthases by heterologous expression in Escherichia coli. J. Biol. Chem. 272 (1997) 9671–9676. [DOI] [PMID: 9092496]
3.  Rüdiger, W., Benz, J. and Guthoff, C. Detection and partial characterization of activity of chlorophyll synthetase in etioplast membranes. Eur. J. Biochem. 109 (1980) 193–200. [DOI] [PMID: 7408876]
[EC 2.5.1.62 created 2003]
 
 
EC 2.5.1.63     
Accepted name: adenosyl-fluoride synthase
Reaction: S-adenosyl-L-methionine + fluoride = 5′-deoxy-5′-fluoroadenosine + L-methionine
Other name(s): fluorinase
Systematic name: S-adenosyl-L-methionine:fluoride adenosyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 438583-16-5
References:
1.  O'Hagan, D., Schaffrath, C., Cobb, S.L., Hamilton, J.T. and Murphy, C.D. Biosynthesis of an organofluorine molecule. Nature 416 (2002) 279. [DOI] [PMID: 11907567]
2.  Dong, C., Huang, F., Deng, H., Schaffrath, C., Specner, J.B., O'Hagan, D. and Naismith, J.H. Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature 427 (2004) 561–565. [DOI] [PMID: 14765200]
[EC 2.5.1.63 created 2003]
 
 
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 2.5.1.65     
Accepted name: O-phosphoserine sulfhydrylase
Reaction: O-phospho-L-serine + hydrogen sulfide = L-cysteine + phosphate
Other name(s): O-phosphoserine(thiol)-lyase
Systematic name: O-phospho-L-serine:hydrogen-sulfide 2-amino-2-carboxyethyltransferase
Comments: A pyridoxal-phosphate protein. The enzyme from Aeropyrum pernix acts on both O-phospho-L-serine and O3-acetyl-L-serine, in contrast with EC 2.5.1.47, cysteine synthase, which acts only on O3-acetyl-L-serine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1071505-11-7
References:
1.  Mino, K. and Ishikawa, K. A novel O-phospho-L-serine sulfhydrylation reaction catalyzed by O-acetylserine sulfhydrylase from Aeropyrum pernix K1. FEBS Lett. 551 (2003) 133–138. [DOI] [PMID: 12965218]
2.  Mino, K. and Ishikawa, K. Characterization of a novel thermostable O-acetylserine sulfhydrylase from Aeropyrum pernix K1. J. Bacteriol. 185 (2003) 2277–2284. [DOI] [PMID: 12644499]
3.  Mino, K. and Ishikawa, K. Crystallization and preliminary X-ray diffraction analysis of O-acetylserine sulfhydrylase from Aeropyrum pernix K1. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 338–340. [PMID: 12554945]
[EC 2.5.1.65 created 2004]
 
 
EC 2.5.1.66     
Accepted name: N2-(2-carboxyethyl)arginine synthase
Reaction: D-glyceraldehyde 3-phosphate + L-arginine = N2-(2-carboxyethyl)-L-arginine + phosphate
For diagram of clavulanate biosynthesis, click here
Other name(s): CEAS; N2-(2-carboxyethyl)arginine synthetase; CEA synthetase; glyceraldehyde-3-phosphate:L-arginine 2-N-(2-hydroxy-3-oxopropyl) transferase (2-carboxyethyl-forming)
Systematic name: glyceraldehyde-3-phosphate:L-arginine N2-(2-hydroxy-3-oxopropyl) transferase (2-carboxyethyl-forming)
Comments: The enzyme requires thiamine diphosphate and catalyses the first step in the clavulanic-acid-biosynthesis pathway. The 2-hydroxy-3-oxo group transferred from glyceraldehyde 3-phosphate is isomerized during transfer to form the 2-carboxyethyl group.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 250207-48-8
References:
1.  Caines, M.E.C., Elkins, J.M., Hewitson, K.S. and Schofield, C.J. Crystal structure and mechanistic implications of N2-(2-carboxyethyl)arginine synthase, the first enzymes in the clavulanic acid biosynthesis pathway. J. Biol. Chem. 279 (2004) 5685–5692. [DOI] [PMID: 14623876]
2.  Khaleeli, N., Li, R. and Townsend, C.A. Origin of the β-lactam carbons in clavulanic acid from an unusual thiamine pyrophosphate-mediated reaction. J. Am. Chem. Soc. 121 (1999) 9223–9224.
[EC 2.5.1.66 created 2004]
 
 
EC 2.5.1.67     
Accepted name: chrysanthemyl diphosphate synthase
Reaction: 2 dimethylallyl diphosphate = diphosphate + chrysanthemyl diphosphate
For diagram of reaction, click here
Other name(s): CPPase
Systematic name: dimethylallyl-diphosphate:dimethylallyl-diphosphate dimethylallyltransferase (chrysanthemyl-diphosphate-forming)
Comments: Requires a divalent metal ion for activity, with Mg2+ being better than Mn2+ [1]. Chrysanthemyl diphosphate is a monoterpene with a non-head-to-tail linkage. It is unlike most monoterpenoids, which are derived from geranyl diphosphate and have isoprene units that are linked head-to-tail. The mechanism of its formation is similar to that of the early steps of squalene and phytoene biosynthesis. Chrysanthemyl diphosphate is the precursor of chrysanthemic acid, the acid half of the pyrethroid insecticides found in chrysanthemums.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Rivera, S.B., Swedlund, B.D., King, G.J., Bell, R.N., Hussey, C.E., Jr., Shattuck-Eidens, D.M., Wrobel, W.M., Peiser, G.D. and Poulter, C.D. Chrysanthemyl diphosphate synthase: isolation of the gene and characterization of the recombinant non-head-to-tail monoterpene synthase from Chrysanthemum cinerariaefolium. Proc. Natl. Acad. Sci. USA 98 (2001) 4373–4378. [DOI] [PMID: 11287653]
2.  Erickson, H.K. and Poulter, C.D. Chrysanthemyl diphosphate synthase. The relationship among chain elongation, branching, and cyclopropanation reactions in the isoprenoid biosynthetic pathway. J. Am. Chem. Soc. 125 (2003) 6886–6888. [DOI] [PMID: 12783539]
[EC 2.5.1.67 created 2007]
 
 
EC 2.5.1.68     
Accepted name: (2Z,6E)-farnesyl diphosphate synthase
Reaction: geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2Z,6E)-farnesyl diphosphate
For diagram of trans-polycis-polyprenol diphosphate biosynthesis, click here
Other name(s): (Z)-farnesyl diphosphate synthase; Z-farnesyl diphosphate synthase
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate geranylcistransferase
Comments: Requires Mg2+ or Mn2+ for activity. The product of this reaction is an intermediate in the synthesis of decaprenyl phosphate, which plays a central role in the biosynthesis of most features of the mycobacterial cell wall, including peptidoglycan, linker unit galactan and arabinan. Neryl diphosphate can also act as substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schulbach, M.C., Mahapatra, S., Macchia, M., Barontini, S., Papi, C., Minutolo, F., Bertini, S., Brennan, P.J. and Crick, D.C. Purification, enzymatic characterization, and inhibition of the Z-farnesyl diphosphate synthase from Mycobacterium tuberculosis. J. Biol. Chem. 276 (2001) 11624–11630. [DOI] [PMID: 11152452]
[EC 2.5.1.68 created 2007, modified 2010]
 
 
EC 2.5.1.69     
Accepted name: lavandulyl diphosphate synthase
Reaction: 2 dimethylallyl diphosphate = diphosphate + lavandulyl diphosphate
For diagram of reaction, click here
Other name(s): FDS-5
Systematic name: dimethylallyl-diphosphate:dimethylallyl-diphosphate dimethylallyltransferase (lavandulyl-diphosphate-forming)
Comments: Lavandulyl diphosphate is a monoterpene with a non-head-to-tail linkage. It is unlike most monoterpenoids, which are derived from geranyl diphosphate and have isoprene units that are linked head-to-tail. When this enzyme is incubated with dimethylallyl diphosphate and isopentenyl diphosphate, it also forms the regular monoterpene geranyl diphosphate [2]. The enzyme from Artemisia tridentata (big sagebrush) forms both lavandulyl diphosphate and chrysanthemyl diphosphate (see EC 2.5.1.67, chrysanthemyl diphosphate synthase) when dimethylally diphosphate is the sole substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Erickson, H.K. and Poulter, C.D. Chrysanthemyl diphosphate synthase. The relationship among chain elongation, branching, and cyclopropanation reactions in the isoprenoid biosynthetic pathway. J. Am. Chem. Soc. 125 (2003) 6886–6888. [DOI] [PMID: 12783539]
2.  Hemmerlin, A., Rivera, S.B., Erickson, H.K. and Poulter, C.D. Enzymes encoded by the farnesyl diphosphate synthase gene family in the Big Sagebrush Artemisia tridentata ssp. spiciformis. J. Biol. Chem. 278 (2003) 32132–32140. [DOI] [PMID: 12782626]
[EC 2.5.1.69 created 2007]
 
 


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