The Enzyme Database

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EC 3.4.22.46     Relevance: 100%
Accepted name: L-peptidase
Reaction: Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys┼Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly┼Arg- and -Lys┼Arg-
Comments: Best known from foot-and-mouth disease virus, but occurs in other aphthoviruses and cardioviruses. Destruction of initiation factor eIF-4G has the effect of shutting off host-cell protein synthesis while allowing synthesis of viral proteins to continue. The tertiary structure reveals a distant relationship to papain and, consistent with this, compound E-64 is inhibitory. Type example of peptidase family C28.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Piccone, M.E., Zellner, M., Kumosinski, T.F., Mason, P.W. and Grubman, M.J. Identification of the active-site residues of the L proteinase of foot-and-mouth disease virus. J. Virol. 69 (1995) 4950–4956. [PMID: 7609064]
2.  Guarné, A., Hampoelz, B., Glaser, W., Carpena, X., Torma, J., Fita, I. and Skern, T. Structural and biochemical features distinguish the foot-and-mouth disease virus leader proteinase from other papain-like enzymes. J. Mol. Biol. 302 (2000) 1227–1240. [DOI] [PMID: 11183785]
[EC 3.4.22.46 created 2001]
 
 
EC 1.1.1.282     Relevance: 85%
Accepted name: quinate/shikimate dehydrogenase
Reaction: (1) L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
(2) shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
For diagram of shikimate and chorismate biosynthesis, click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram). The use of the term ’5-dehydroquinate’ for this compound is based on an earlier system of numbering.
Other name(s): YdiB
Systematic name: L-quinate:NAD(P)+ 3-oxidoreductase
Comments: This is the second shikimate dehydrogenase enzyme found in Escherichia coli and differs from EC 1.1.1.25, shikimate dehydrogenase, in that it can use both quinate and shikimate as substrate and either NAD+ or NADP+ as acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Michel, G., Roszak, A.W., Sauvé, V., Maclean, J., Matte, A., Coggins, J.R., Cygler, M. and Lapthorn, A.J. Structures of shikimate dehydrogenase AroE and its paralog YdiB. A common structural framework for different activities. J. Biol. Chem. 278 (2003) 19463–19472. [DOI] [PMID: 12637497]
2.  Benach, J., Lee, I., Edstrom, W., Kuzin, A.P., Chiang, Y., Acton, T.B., Montelione, G.T. and Hunt, J.F. The 2.3-Å crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase. J. Biol. Chem. 278 (2003) 19176–19182. [DOI] [PMID: 12624088]
[EC 1.1.1.282 created 2004]
 
 
EC 1.1.99.25      
Transferred entry: quinate dehydrogenase (pyrroloquinoline-quinone). Now EC 1.1.5.8, quinate dehydrogenase (quinone)
[EC 1.1.99.25 created 1992, modified 2004, deleted 2010]
 
 
EC 4.2.1.10     Relevance: 81.7%
Accepted name: 3-dehydroquinate dehydratase
Reaction: 3-dehydroquinate = 3-dehydroshikimate + H2O
For diagram of shikimate and chorismate biosynthesis, click here and for mechanism of reaction, click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram). The use of the term ’5-dehydroquinate’ for this compound is based on an earlier system of numbering.
Other name(s): 3-dehydroquinate hydrolase; DHQase; dehydroquinate dehydratase; 3-dehydroquinase; 5-dehydroquinase; dehydroquinase; 5-dehydroquinate dehydratase; 5-dehydroquinate hydro-lyase; 3-dehydroquinate hydro-lyase
Systematic name: 3-dehydroquinate hydro-lyase (3-dehydroshikimate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9012-66-2
References:
1.  Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XII. Conversion of 5-dehydroquinic acid to 5-dehydroshikimic acid by 5-dehydroquinase. Biochim. Biophys. Acta 15 (1954) 54–61. [DOI] [PMID: 13198937]
2.  Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XIII. Conversion of quinic acid to 5-dehydroquinic acid by quinic dehydrogenase. Biochim. Biophys. Acta 15 (1954) 268–280. [DOI] [PMID: 13208693]
[EC 4.2.1.10 created 1961, modified 1976]
 
 
EC 2.1.1.113     Relevance: 80.3%
Accepted name: site-specific DNA-methyltransferase (cytosine-N4-specific)
Reaction: S-adenosyl-L-methionine + DNA cytosine = S-adenosyl-L-homocysteine + DNA N4-methylcytosine
Other name(s): modification methylase; restriction-modification system; DNA[cytosine-N4]methyltransferase; m4C-forming MTase; S-adenosyl-L-methionine:DNA-cytosine 4-N-methyltransferase
Systematic name: S-adenosyl-L-methionine:DNA-cytosine N4-methyltransferase
Comments: This is a large group of enzymes, most of which, with enzymes of similar site specificity listed as EC 3.1.21.3 (type 1 site-specific deoxyribonuclease), EC 3.1.21.4 (type II site-specific deoxyribonuclease) or EC 3.1.21.5 (type III site-specific deoxyribonuclease), form so-called ’restriction-modification systems’. A complete listing of all of these enzymes has been produced by R.J. Roberts and is available on-line at http://rebase.neb.com/rebase/rebase.html.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 169592-50-1
References:
1.  Kessler, C. and Manta, V. Specificity of restriction endonucleases and DNA modification methyltransferases: a review. Gene 92 (1990) 1–248. [DOI] [PMID: 2172084]
2.  Klimasauskas, S., Timinskas, A., Menkevicius, S., Butkiene, D., Butkus, V. and Janulaitis, A. Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases. Nucleic Acids Res. 17 (1989) 9823–9832. [DOI] [PMID: 2690010]
3.  Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331–2365. [PMID: 2159140]
4.  Yuan, R. Structure and mechanism of multifunctional restriction endonucleases. Annu. Rev. Biochem. 50 (1981) 285–319. [DOI] [PMID: 6267988]
[EC 2.1.1.113 created 1992]
 
 
EC 4.2.3.4     Relevance: 71.4%
Accepted name: 3-dehydroquinate synthase
Reaction: 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate + phosphate
For diagram of shikimate and chorismate biosynthesis, click here and for mechanism of reaction, click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram). The use of the term ’5-dehydroquinate’ for this compound is based on an earlier system of numbering.
Other name(s): 5-dehydroquinate synthase; 5-dehydroquinic acid synthetase; dehydroquinate synthase; 3-dehydroquinate synthetase; 3-deoxy-arabino-heptulosonate-7-phosphate phosphate-lyase (cyclizing); 3-deoxy-arabino-heptulonate-7-phosphate phosphate-lyase (cyclizing); 3-deoxy-arabino-heptulonate-7-phosphate phosphate-lyase (cyclizing; 3-dehydroquinate-forming)
Systematic name: 3-deoxy-D-arabino-hept-2-ulosonate-7-phosphate phosphate-lyase (cyclizing; 3-dehydroquinate-forming)
Comments: Requires Co2+ and bound NAD+. The hydrogen atoms on C-7 of the substrate are retained on C-2 of the product.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37211-77-1
References:
1.  Rotenberg, S.L. and Sprinson, D.B. Mechanism and stereochemistry of 5-dehydroquinate synthetase. Proc. Natl. Acad. Sci. USA 67 (1970) 1669–1672. [DOI] [PMID: 5275368]
2.  Srinivasan, P.R., Rothschild, J. and Sprinson, D.B. The enzymic conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate to 5-dehydroquinate. J. Biol. Chem. 238 (1963) 3176–3182. [PMID: 14085358]
3.  Bender, S.L., Mehdi, S. and Knowles, J.R. Dehydroquinate synthase: the role of divalent metal cations and of nicotinamide adenine dinucleotide in catalysis. Biochemistry 28 (1989) 7555–7560. [PMID: 2514789]
4.  Carpenter, E.P., Hawkins, A.R., Frost, J.W. and Brown, K.A. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Nature 394 (1998) 299–302. [DOI] [PMID: 9685163]
[EC 4.2.3.4 created 1978 as EC 4.6.1.3, transferred 2000 to EC 4.2.3.4, modified 2002]
 
 
EC 2.4.2.32     Relevance: 66.4%
Accepted name: dolichyl-phosphate D-xylosyltransferase
Reaction: UDP-D-xylose + dolichyl phosphate = UDP + dolichyl D-xylosyl phosphate
Glossary: dolichol
Systematic name: UDP-D-xylose:dolichyl-phosphate D-xylosyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Waechter, C.J., Lucas, J.J. and Lennarz, W.J. Evidence for xylosyl lipids as intermediates in xylosyl transfers in hen oviduct membranes. Biochem. Biophys. Res. Commun. 56 (1974) 343–350. [DOI] [PMID: 4823870]
[EC 2.4.2.32 created 1984, modified 2003]
 
 
EC 4.6.1.14     Relevance: 63.7%
Accepted name: glycosylphosphatidylinositol diacylglycerol-lyase
Reaction: 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol = 6-(α-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate + 1,2-diacyl-sn-glycerol
For diagram of glycosylphosphatidyl-myo-inositol biosynthesis, click here
Other name(s): (glycosyl)phosphatidylinositol-specific phospholipase C; GPI-PLC; GPI-specific phospholipase C; VSG-lipase; glycosyl inositol phospholipid anchor-hydrolyzing enzyme; glycosylphosphatidylinositol-phospholipase C; glycosylphosphatidylinositol-specific phospholipase C; variant-surface-glycoprotein phospholipase C; 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol diacylglycerol-lyase (1,2-cyclic-phosphate-forming)
Systematic name: 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol 1,2-diacyl-sn-glycerol-lyase [6-(α-D-glucosaminyl)-1D-myo-inositol 1,2-cyclic phosphate-forming]
Comments: This enzyme is also active when O-4 of the glucosamine is substituted by carrying the oligosaccharide that can link a protein to the structure. It therefore cleaves proteins from the lipid part of the glycosylphostphatidylinositol (GPI) anchors. In some cases, the long-chain acyl group at the sn-1 position of glycerol is replaced by an alkyl or alk-1-enyl group. In other cases, the diacylglycerol is replaced by ceramide (see Lip-1.4 and Lip-1.5 for definition). The only characterized enzyme with this specificity is from Trypanosoma brucei, where the acyl groups are myristoyl, but the function of the trypanosome enzyme is unknown. Substitution on O-2 of the inositol blocks action of this enzyme. It is not identical with EC 3.1.4.50, glycosylphosphatidylinositol phospholipase D.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 129070-68-4
References:
1.  Hereld, D., Krakow, J.L., Bangs, J.D., Hart, G.W. and Englund, P.T. A phospholipase C from Trypanosoma brucei which selectively cleaves the glycolipid on the variant surface glycoprotein. J. Biol. Chem. 261 (1986) 13813–13819. [PMID: 3759991]
2.  Carnall, N., Webb, H. and Carrington, M. Mutagenesis study of the glycosylphosphatidylinositol phospholipase C of Trypanosoma brucei. Mol. Biochem. Parasitol. 90 (1997) 423–432. [DOI] [PMID: 9476790]
3.  Armah, D.A. and Mensa-Wilmot, K. Tetramerization of glycosylphosphatidylinositol-specific phospholipase C from Trypanosoma brucei. J. Biol. Chem. 275 (2000) 19334–19342. [DOI] [PMID: 10764777]
[EC 4.6.1.14 created 1989 as EC 3.1.4.47, transferred 2002 to EC 4.6.1.14]
 
 
EC 2.3.1.159     Relevance: 62.3%
Accepted name: acridone synthase
Reaction: 3 malonyl-CoA + N-methylanthraniloyl-CoA = 4 CoA + 1,3-dihydroxy-N-methylacridone + 3 CO2
For diagram of acridone alkaloid biosynthesis, click here
Systematic name: malonyl-CoA:N-methylanthraniloyl-CoA malonyltransferase (cyclizing)
Comments: Belongs to a superfamily of plant polyketide synthases. Has many similarities to chalcone and stilbene synthases (see reaction synthesis)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 99085-53-7
References:
1.  Baumert, A., Maier, W., Gröger, D. and Deutzmann, R. Purification and properties of acridone synthase from cell suspension cultures of Ruta graveolens L. Z. Naturforsch. C: Biosci. 49 (1994) 26–32. [PMID: 8148006]
2.  Maier, W., Baumert, A., Schumann, B., Furukawa, H. and Gröger, D. Synthesis of 1,3-dihydroxy-N-methylacridone and its conversion to rutacridone by cell-free extracts of Ruta-graveolens cell cultures. Phytochemistry 32 (1993) 691–698.
3.  Lukačin, R., Springob, K., Urbanke, C., Ernwein, C., Schroder, G., Schroder, J. and Matern, U. Native acridone synthases I and II from Ruta graveolens L. form homodimers. FEBS Lett. 448 (1999) 135–140. [DOI] [PMID: 10217426]
4.  Junghanns, K.T., Kneusel, R.E., Groger, D. and Matern, U. Differential regulation and distribution of acridone synthase in Ruta graveolens. Phytochemistry 49 (1998) 403–411. [DOI] [PMID: 9747538]
[EC 2.3.1.159 created 2002]
 
 
EC 2.4.1.99     Relevance: 61.1%
Accepted name: sucrose:sucrose fructosyltransferase
Reaction: 2 sucrose = D-glucose + β-D-fructofuranosyl-(2→1)-β-D-fructofuranosyl α-D-glucopyranoside
Other name(s): SST; sucrose:sucrose 1-fructosyltransferase; sucrose-sucrose 1-fructosyltransferase; sucrose 1F-fructosyltransferase; sucrose:sucrose 1F-β-D-fructosyltransferase
Systematic name: sucrose:sucrose 1′-β-D-fructosyltransferase
Comments: For definition of the prime in the systematic name, see 2-Carb-36.2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 73379-56-3
References:
1.  Henry, R.J. and Darbyshire, B. Sucrose:sucrose fructosyltransferase and fructan:fructan fructosyltransferase from Allium cepa. Phytochemistry 19 (1980) 1017–1020.
2.  Lüscher, M., Hochstrasser, U., Vogel, G., Aeschbacher, R., Galati, V., Nelson, C.J., Boller, T. and Wiemken, A. Cloning and functional analysis of sucrose:sucrose 1-fructosyltransferase from tall fescue. Plant Physiol. 124 (2000) 1217–1228. [PMID: 11080298]
[EC 2.4.1.99 created 1981, modified 2004]
 
 
EC 1.14.20.1     Relevance: 60.5%
Accepted name: deacetoxycephalosporin-C synthase
Reaction: penicillin N + 2-oxoglutarate + O2 = deacetoxycephalosporin C + succinate + CO2 + H2O
For diagram of penicillin-N and deacetoxycephalosporin-C biosynthesis, click here
Other name(s): DAOCS; penicillin N expandase; DAOC synthase
Systematic name: penicillin-N,2-oxoglutarate:oxygen oxidoreductase (ring-expanding)
Comments: Forms part of the penicillin biosynthesis pathway (for pathway, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 85746-10-7
References:
1.  Cantwell, C., Beckmann, R., Whiteman, P., Queener, S.W. and Abraham, E.P. Isolation of deacetoxycephalosporin-c from fermentation broths of Penicillium chrysogenum transformants - construction of a new fungal biosynthetic-pathway. Proc. R. Soc. Lond. B Biol. Sci. 248 (1992) 283–289. [DOI] [PMID: 1354366]
2.  Lee, H.J., Lloyd, M.D., Harlos, K., Clifton, I.J., Baldwin, J.E. and Schofield, C.J. Kinetic and crystallographic studies on deacetoxycephalosporin C synthase (DAOCS). J. Mol. Biol. 308 (2001) 937–948. [DOI] [PMID: 11352583]
3.  Yeh, W.K., Ghag, S.K. and Queener, S.W. Enzymes for epimerization of isopenicillin N, ring expansion of penicillin N, and 3′-hydroxylation of deacetoxycephalosporin C. Function, evolution, refolding, and enzyme engineering. Ann. N.Y. Acad. Sci. 672 (1992) 396–408.
4.  Valegaard, K., van Scheltinga, A.C.T., Lloyd, M.D., Hara, T., Ramaswamy, S., Perrakis, A., Thompson, A., Lee, H.-J., Baldwin, J.E., Schofield, C.J., Hajdu, J. and Andersson, I. Structure of a cephalosporin synthase. Nature 394 (1998) 805–809. [DOI] [PMID: 9723623]
5.  Dotzlaf, J.E. and Yeh, W.K. Purification and properties of deacetoxycephalosporin C synthase from recombinant Escherichia coli and its comparison with the native enzyme purified from Streptomyces clavuligerus. J. Biol. Chem. 264 (1989) 10219–10227. [PMID: 2656705]
[EC 1.14.20.1 created 2002]
 
 
EC 5.1.1.17     Relevance: 58.8%
Accepted name: isopenicillin-N epimerase
Reaction: isopenicillin N = penicillin N
For diagram of penicillin-N and deacetoxycephalosporin-C biosynthesis, click here
Systematic name: penicillin-N 5-amino-5-carboxypentanoyl-epimerase
Comments: This enzyme contains pyridoxal phosphate. Epimerization at C-5 of the 5-amino-5-carboxypentanoyl group to form penicillin N is required to make a substrate for EC 1.14.20.1, deactoxycephalosporin-C synthase, to produce cephalosporins. Forms part of the penicillin biosynthesis pathway (for pathway, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 88201-43-8
References:
1.  Usui, S. and Yu, C.-A. Purification and properties of isopenicillin-N epimerase from Streptomyces clavuligerus. Biochim. Biophys. Acta 999 (1989) 78–85. [DOI] [PMID: 2804141]
2.  Laiz, L., Liras, P., Castro, J.M. and Martín, J.F. Purification and characterization of the isopenicillin-N epimerase from Nocardia lactamdurans. J. Gen. Microbiol. 136 (1990) 663–671.
3.  Cantwell, C., Beckmann, R., Whiteman, P., Queener, S.W. and Abraham, E.P. Isolation of deacetoxycephalosporin-c from fermentation broths of Penicillium chrysogenum transformants - construction of a new fungal biosynthetic-pathway. Proc. R. Soc. Lond. B Biol. Sci. 248 (1992) 283–289. [DOI] [PMID: 1354366]
4.  Yeh, W.K., Ghag, S.K. and Queener, S.W. Enzymes for epimerization of isopenicillin N, ring expansion of penicillin N, and 3′-hydroxylation of deacetoxycephalosporin C. Function, evolution, refolding, and enzyme engineering. Ann. N.Y. Acad. Sci. 672 (1992) 396–408.
[EC 5.1.1.17 created 2002]
 
 
EC 2.4.2.34     Relevance: 58.1%
Accepted name: indolylacetylinositol arabinosyltransferase
Reaction: UDP-L-arabinose + (indol-3-yl)acetyl-1D-myo-inositol = UDP + (indol-3-yl)acetyl-myo-inositol 3-L-arabinoside
Other name(s): arabinosylindolylacetylinositol synthase; UDP-L-arabinose:indol-3-ylacetyl-myo-inositol L-arabinosyltransferase; UDP-L-arabinose:(indol-3-yl)acetyl-myo-inositol L-arabinosyltransferase
Systematic name: UDP-L-arabinose:(indol-3-yl)acetyl-1D-myo-inositol L-arabinosyltransferase
Comments: The position of acylation is indeterminate because of the ease of acyl transfer between hydroxy groups. For a diagram showing the biosynthesis of UDP-L-arabinose, click here.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 84720-96-7
References:
1.  Corcuera, L.J. and Bandurski, R.S. Biosynthesis of indol-3-yl-acetyl-myo-inositol arabinoside in kernels of Zea mays L. Plant Physiol. 70 (1982) 1664–1666. [PMID: 16662740]
[EC 2.4.2.34 created 1986, modified 2003]
 
 
EC 3.4.13.22     Relevance: 57.9%
Accepted name: D-Ala-D-Ala dipeptidase
Reaction: D-Ala-D-Ala + H2O = 2 D-Ala
Other name(s): D-alanyl-D-alanine dipeptidase; vanX D-Ala-D-Ala dipeptidase; VanX
Comments: A Zn2+-dependent enzyme [4]. The enzyme protects Enterococcus faecium from the antibiotic vancomycin, which can bind to the -D-Ala-D-Ala sequence at the C-terminus of the peptidoglycan pentapeptide (see diagram). This enzyme reduces the availability of the free dipeptide D-Ala-D-Ala, which is the precursor for this pentapeptide sequence, allowing D-Ala-(R)-lactate (for which vancomycin has much less affinity) to be added to the cell wall instead [2,3]. The enzyme is stereospecific, as L-Ala-L-Ala, D-Ala-L-Ala and L-Ala-D-Ala are not substrates [2]. Belongs in peptidase family M15.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Reynolds, P.E., Depardieu, F., Dutka-Malen, S., Arthur, M. and Courvalin, P. Glycopeptide resistance mediated by enterococcal transposon Tn1546 requires production of VanX for hydrolysis of D-alanyl-D-alanine. Mol. Microbiol. 13 (1994) 1065–1070. [DOI] [PMID: 7854121]
2.  Wu, Z., Wright, G.D. and Walsh, C.T. Overexpression, purification, and characterization of VanX, a D-, D-dipeptidase which is essential for vancomycin resistance in Enterococcus faecium BM4147. Biochemistry 34 (1995) 2455–2463. [PMID: 7873524]
3.  McCafferty, D.G., Lessard, I.A. and Walsh, C.T. Mutational analysis of potential zinc-binding residues in the active site of the enterococcal D-Ala-D-Ala dipeptidase VanX. Biochemistry 36 (1997) 10498–10505. [DOI] [PMID: 9265630]
4.  Bussiere, D.E., Pratt, S.D., Katz, L., Severin, J.M., Holzman, T. and Park, C.H. The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance. Mol. Cell. 2 (1998) 75–84. [DOI] [PMID: 9702193]
5.  Tan, A.L., Loke, P. and Sim, T.S. Molecular cloning and functional characterisation of VanX, a D-alanyl-D-alanine dipeptidase from Streptomyces coelicolor A3(2). Res. Microbiol. 153 (2002) 27–32. [DOI] [PMID: 11881895]
6.  Matthews, M.L., Periyannan, G., Hajdin, C., Sidgel, T.K., Bennett, B. and Crowder, M.W. Probing the reaction mechanism of the D-ala-D-ala dipeptidase, VanX, by using stopped-flow kinetic and rapid-freeze quench EPR studies on the Co(II)-substituted enzyme. J. Am. Chem. Soc. 128 (2006) 13050–13051. [DOI] [PMID: 17017774]
[EC 3.4.13.22 created 2006]
 
 
EC 1.21.3.1     Relevance: 57.2%
Accepted name: isopenicillin-N synthase
Reaction: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + O2 = isopenicillin N + 2 H2O
For diagram of penicillin-N and deacetoxycephalosporin-C biosynthesis, click here and for possible mechanism of reaction, click here
Other name(s): isopenicillin N synthetase
Systematic name: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine:oxygen oxidoreductase (cyclizing)
Comments: Forms part of the penicillin biosynthesis pathway (for pathway, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 78642-31-6
References:
1.  Huffman, G.W., Gesellchen, P.D., Turner, J.R., Rothenberger, R.B., Osborne, H.E., Miller, F.D., Chapman, J.L. and Queener, S.W. Substrate specificity of isopenicillin N synthase. J. Med. Chem. 35 (1992) 1897–1914. [PMID: 1588566]
2.  Roach, P.L., Clifton, I.J., Fulop, V., Harlos, K., Barton, G.J., Hajdu, J., Andersson, I., Schofield, C.J. and Baldwin, J.E. Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. Nature 375 (1995) 700–704. [DOI] [PMID: 7791906]
[EC 1.21.3.1 created 2002]
 
 
EC 2.7.7.60     Relevance: 56.8%
Accepted name: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Reaction: CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol
For diagram of non-mevalonate terpenoid biosynthesis, click here
Other name(s): MEP cytidylyltransferase
Systematic name: CTP:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Comments: The enzyme from Escherichia coli requires Mg2+ or Mn2+. ATP or UTP can replace CTP, but both are less effective. GTP and TTP are not substrates. Forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis (for diagram, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 251990-59-7
References:
1.  Rohdich, F., Wungsintaweekul, J., Fellermeier, M., Sagner, S., Herz, S., Kis, K., Eisenreich, W., Bacher, A. and Zenk, M.H. Cytidine 5′-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erithritol. Proc. Natl Acad. Sci. USA 96 (1999) 11758–11763. [DOI] [PMID: 10518523]
2.  Kuzuyama, T., Takagi, M., Kaneda, K., Dairi, T. and Seto, H. Formation of 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol from 2-C-methyl-D-erythritol 4-phosphate by 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, a new enzyme in the nonmevalonate pathway. Tetrahedron Lett. 41 (2000) 703–706.
[EC 2.7.7.60 created 2001]
 
 
EC 1.17.4.3      
Transferred entry: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase. As ferredoxin and not protein-disulfide is now known to take part in the reaction, the enzyme has been transferred to EC 1.17.7.1, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase.
[EC 1.17.4.3 created 2003, deleted 2009]
 
 
EC 3.3.1.1     Relevance: 56.3%
Accepted name: adenosylhomocysteinase
Reaction: S-adenosyl-L-homocysteine + H2O = L-homocysteine + adenosine
For diagram of reaction mechanism, click here
Other name(s): S-adenosylhomocysteine synthase; S-adenosylhomocysteine hydrolase (ambiguous); adenosylhomocysteine hydrolase; S-adenosylhomocysteinase; SAHase; AdoHcyase
Systematic name: S-adenosyl-L-homocysteine hydrolase
Comments: The enzyme contains one tightly bound NAD+ per subunit. This appears to bring about a transient oxidation at C-3′ of the 5′-deoxyadenosine residue, thus labilizing the thioether bond [2] (for mechanism, click here), cf. EC 5.5.1.4, inositol-3-phosphate synthase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9025-54-1
References:
1.  de la Haba, G. and Cantoni, G.L. The enzymatic synthesis of S-adenosyl-L-homocysteine from adenosine and homocysteine. J. Biol. Chem. 234 (1959) 603–608. [PMID: 13641268]
2.  Palmer, J.L. and Abeles, R.H. The mechanism of action of S-adenosylhomocysteinase. J. Biol. Chem. 254 (1979) 1217–1226. [PMID: 762125]
[EC 3.3.1.1 created 1961, modified 2004]
 
 
EC 2.7.1.148     Relevance: 55.3%
Accepted name: 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase
Reaction: ATP + 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol = ADP + 2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol
For diagram of non-mevalonate terpenoid biosynthesis, click here
Other name(s): CDP-ME kinase
Systematic name: ATP:4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol 2-phosphotransferase
Comments: The enzyme from Escherichia coli requires Mg2+ or Mn2+. Forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis (for diagram, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 263016-77-9
References:
1.  Lüttgen, H., Rohdich, F., Herz, S., Wungsintaweekul, J., Hecht, S., Schuhr, C.A., Fellermeier, M., Sagner, S., Zenk, M.H., Bacher, A. and Eisenreich, W. Biosynthesis of terpenoids: YchB protein of Escherichia coli phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erithritol. Proc. Natl. Acad. Sci. USA 97 (2000) 1062–1067. [DOI] [PMID: 10655484]
2.  Kuzuyama, T., Takagi, M., Kaneda, K., Watanabe, H., Dairi, T. and Seto, H. Studies on the nonmevalonate pathway: conversion of 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol to its 2-phospho derivative by 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase. Tetrahedron Lett. 41 (2000) 2925–2928.
[EC 2.7.1.148 created 2001]
 
 
EC 5.2.1.8     Relevance: 54%
Accepted name: peptidylprolyl isomerase
Reaction: peptidylproline (ω=180) = peptidylproline (ω=0)
Glossary: For definition of ω, click here
Other name(s): PPIase; cyclophilin [misleading, see comments]; peptide bond isomerase; peptidyl-prolyl cis-trans isomerase
Systematic name: peptidylproline cis-trans-isomerase
Comments: The first type of this enzyme found [1] proved to be the protein cyclophilin, which binds the immunosuppressant cyclosporin A. Other distinct families of the enzyme exist, one being FK-506 binding proteins (FKBP) and another that includes parvulin from Escherichia coli. The three families are structurally unrelated and can be distinguished by being inhibited by cyclosporin A, FK-506 and 5-hydroxy-1,4-naphthoquinone, respectively.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 95076-93-0
References:
1.  Fischer, G. and Bang, H. The refolding of urea-denatured ribonuclease A is catalyzed by peptidyl-prolyl cis-trans isomerase. Biochim. Biophys. Acta 828 (1985) 39–42. [DOI] [PMID: 3882150]
2.  Fischer, G., Bang, H. and Mech, C. [Determination of enzymatic catalysis for the cis-trans-isomerization of peptide binding in proline-containing peptides] Biomed. Biochim. Acta 43 (1984) 1101–1111. [PMID: 6395866]
3.  Fischer, G., Wittmann-Liebold, B., Lang, K., Kiefhaber, T. and Schmid, F.X. Cyclophilin and peptidyl-prolyl cis-trans isomerase are probably identical proteins. Nature 337 (1989) 476–478. [DOI] [PMID: 2492638]
4.  Takahashi, N., Hayano, T. and Suzuki, M. Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin. Nature 337 (1989) 473–475. [DOI] [PMID: 2644542]
5.  Hennig, L., Christner, C., Kipping, M., Schelbert, B., Rucknagel, K.P., Grabley, S., Kullertz, G. and Fischer, G. Selective inactivation of parvulin-like peptidyl-prolyl cis/trans isomerases by juglone. Biochemistry 37 (1998) 5953–5960. [DOI] [PMID: 9558330]
6.  Fischer, G. Peptidyl-prolyl cis/trans isomerases and their effectors. Angew. Chem. Int. Ed. Engl. 33 (1994) 1415–1436.
7.  Harrison, R.K. and Stein, R.L. Substrate specificities of the peptidyl prolyl cis-trans isomerase activities of cyclophilin and FK-506 binding protein: evidence for the existence of a family of distinct enzymes. Biochemistry 29 (1990) 3813–3816. [PMID: 1693856]
8.  Eisenmesser, E.Z., Bosco, D.A., Akke, M. and Kern, D. Enzyme dynamics during catalysis. Science 295 (2002) 1520–1523. [DOI] [PMID: 11859194]
[EC 5.2.1.8 created 1989, modified 2002]
 
 
EC 4.6.1.17     Relevance: 53.2%
Accepted name: cyclic pyranopterin monophosphate synthase
Reaction: (8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate = cyclic pyranopterin phosphate + diphosphate
Other name(s): MOCS1B (gene name); moaC (gene name); cnx3 (gene name)
Systematic name: (8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate lyase (cyclic pyranopterin phosphate-forming)
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). In bacteria and plants the reaction is catalysed by MoaC and Cnx3, respectively. In mammals the reaction is catalysed by the MOCS1B domain of the bifuctional MOCS1 protein, which also catalyses EC 4.1.99.22, GTP 3′,8-cyclase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Rieder, C., Eisenreich, W., O'Brien, J., Richter, G., Götze, E., Boyle, P., Blanchard, S., Bacher, A. and Simon, H. Rearrangement reactions in the biosynthesis of molybdopterin - an NMR study with multiply 13C/15N labelled precursors. Eur. J. Biochem. 255 (1998) 24–36. [DOI] [PMID: 9692897]
2.  Wuebbens, M.M. and Rajagopalan, K.V. Investigation of the early steps of molybdopterin biosynthesis in Escherichia coli through the use of in vivo labeling studies. J. Biol. Chem. 270 (1995) 1082–1087. [DOI] [PMID: 7836363]
3.  Hover, B.M., Tonthat, N.K., Schumacher, M.A. and Yokoyama, K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. USA 112 (2015) 6347–6352. [DOI] [PMID: 25941396]
[EC 4.6.1.17 created 2011 as EC 4.1.99.18, part transferred 2016 to EC 4.6.1.17]
 
 
EC 6.3.2.4     Relevance: 52.5%
Accepted name: D-alanine—D-alanine ligase
Reaction: ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
Other name(s): MurE synthetase [ambiguous]; alanine:alanine ligase (ADP-forming); alanylalanine synthetase
Systematic name: D-alanine:D-alanine ligase (ADP-forming)
Comments: Involved with EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase) or EC 6.3.2.13 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—2,6-diaminopimelate ligase), EC 6.3.2.8 (UDP-N-acetylmuramate—L-alanine ligase), EC 6.3.2.9 (UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase) and EC 6.3.2.10 (UDP-N-acetylmuramoyl-tripeptide—D-alanyl-D-alanine ligase) in the synthesis of a cell-wall peptide (click here for diagram).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-63-6
References:
1.  Ito, E. and Strominger, J.L. Enzymatic synthesis of the peptide in bacterial uridine nucleotides. II. Enzymatic synthesis and addition of D-alanyl-D-alanine. J. Biol. Chem. 237 (1962) 2696–2703.
2.  Neuhaus, F.C. Kinetic studies on D-Ala-D-Ala synthetase. Fed. Proc. 21 (1962) 229.
3.  van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503–519. [PMID: 11699883]
[EC 6.3.2.4 created 1961, modified 2002]
 
 
EC 1.3.1.72     Relevance: 52.1%
Accepted name: Δ24-sterol reductase
Reaction: 5α-cholest-7-en-3β-ol + NADP+ = 5α-cholesta-7,24-dien-3β-ol + NADPH + H+
For diagram of sterol-sidechain modification, click here
Glossary: desmosterol = cholesta-5,24-dien-3β-ol
lanosterol = 4,4,14-trimethyl-5α-cholesta-8,24-dien-3β-ol
zymostrol = 5α-cholesta-8,24-dien-3β-ol
Other name(s): lanosterol Δ24-reductase
Systematic name: sterol:NADP+ Δ24-oxidoreductase
Comments: Acts on a range of steroids with a 24(25)-double bond, including lanosterol, desmosterol and zymosterol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9033-57-2
References:
1.  Bae, S.H. and Paik, Y.K. Cholesterol biosynthesis from lanosterol: development of a novel assay method and characterization of rat liver microsomal lanosterol Δ24-reductase. Biochem. J. 326 (1997) 609–616. [PMID: 9291139]
[EC 1.3.1.72 created 2001]
 
 
EC 3.2.1.162     Relevance: 51.5%
Accepted name: λ-carrageenase
Reaction: Endohydrolysis of (1→4)-β-linkages in the backbone of λ-carrageenan, resulting in the tetrasaccharide α-D-Galp2,6S2-(1→3)-β-D-Galp2S-(1→4)-α-D-Galp2,6S2-(1→3)-D-Galp2S
For diagram of reaction, click here
Glossary: For diagram of the structures of carrageenans, click here
Other name(s): endo-β-1,4-carrageenose 2,6,2′-trisulfate-hydrolase
Systematic name: endo-(1→4)-β-carrageenose 2,6,2′-trisulfate-hydrolase
Comments: The enzyme from Pseudoalteromonas sp. is specific for λ-carrageenan. ι-Carrageenan (see EC 3.2.1.157, ι-carrageenase), κ-carrageenan (see EC 3.2.1.83, κ-carrageenase), agarose and porphyran are not substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ohta, Y. and Hatada, Y. A novel enzyme, λ-carrageenase, isolated from a deep-sea bacterium. J. Biochem. (Tokyo) 140 (2006) 475–481. [DOI] [PMID: 16926183]
[EC 3.2.1.162 created 2007]
 
 
EC 2.7.7.37     Relevance: 51.4%
Accepted name: aldose-1-phosphate nucleotidyltransferase
Reaction: NDP + α-D-aldose 1-phosphate = phosphate + NDP-aldose
For diagram of UDP-L-arabinose, UDP-galacturonate and UDP-xylose biosynthesis, click here
Other name(s): sugar-1-phosphate nucleotidyltransferase; NDPaldose phosphorylase; glucose 1-phosphate inosityltransferase; NDP sugar phosphorylase; nucleoside diphosphosugar phosphorylase; sugar phosphate nucleotidyltransferase; nucleoside diphosphate sugar:orthophosphate nucleotidyltransferase; sugar nucleotide phosphorylase; NDP:aldose-1-phosphate nucleotidyltransferase
Systematic name: NDP:α-D-aldose-1-phosphate nucleotidyltransferase
Comments: The enzyme works on a variety of α-D-aldose 1-phosphates and β-L-aldose 1-phosphates (which have the same anomeric configuration as the former; see 2-Carb-6.2).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9033-61-8
References:
1.  Cabib, E., Carminatti, H. and Woyskovsky, N.M. Phosphorolysis of the pyrophosphate bond of sugar nucleotides. II. Purification and properties of the enzyme. J. Biol. Chem. 240 (1965) 2114–2121. [PMID: 14299635]
[EC 2.7.7.37 created 1972, modified 1986]
 
 
EC 2.1.1.72     Relevance: 50.8%
Accepted name: site-specific DNA-methyltransferase (adenine-specific)
Reaction: S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N6-methyladenine in DNA
Other name(s): modification methylase; restriction-modification system
Systematic name: S-adenosyl-L-methionine:adenine in DNA N6-methyltransferase
Comments: This is a large group of enzymes, most of which form so-called ’restriction-modification systems’ with nucleases that possess similar site specificity [the nucleases are listed as either EC 3.1.21.3 (type 1 site-specific deoxyribonuclease), EC 3.1.21.4 (type II site-specific deoxyribonuclease) or EC 3.1.21.5 (type III site-specific deoxyribonuclease)]. A complete listing of all of these enzymes has been produced by R.J. Roberts and is available on-line at http://rebase.neb.com/rebase/rebase.html.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 69553-52-2
References:
1.  Kessler, C. and Manta, V. Specificity of restriction endonucleases and DNA modification methyltransferases: a review. Gene 92 (1990) 1–248. [DOI] [PMID: 2172084]
2.  Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331–2365. [PMID: 2159140]
3.  Yuan, R. Structure and mechanism of multifunctional restriction endonucleases. Annu. Rev. Biochem. 50 (1981) 285–319. [DOI] [PMID: 6267988]
[EC 2.1.1.72 created 1984]
 
 
EC 4.6.1.12     Relevance: 50.7%
Accepted name: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Reaction: 2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
For diagram of non-mevalonate terpenoid biosynthesis, click here
Other name(s): MECDP-synthase; 2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol CMP-lyase (cyclizing)
Systematic name: 2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol CMP-lyase (cyclizing; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate-forming)
Comments: The enzyme from Escherichia coli requires Mg2+ or Mn2+. Forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis (for diagram, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 287480-92-6
References:
1.  Herz, S., Wungsintaweekul, J., Schuhr, C.A., Hecht, S., Lüttgen, H., Sagner, S., Fellermeier, M., Eisenreich, W., Zenk, M.H., Bacher, A. and Rohdich, F. Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erithritol 2-phosphate to 2-C-methyl-D-erithritol 2,4-cyclodiphosphate. Proc. Natl. Acad. Sci. USA 97 (2000) 2486–2490. [DOI] [PMID: 10694574]
2.  Takagi, M., Kuzuyama, T., Kaneda, K., Watanabe, H., Dairi, T. and Seto, H. Studies on the nonmevalonate pathway: Formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate from 2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol. Tetrahedron Lett. 41 (2000) 3395–3398.
[EC 4.6.1.12 created 2001]
 
 
EC 6.3.2.26     Relevance: 50.4%
Accepted name: N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase
Reaction: 3 ATP + L-2-aminohexanedioate + L-cysteine + L-valine + H2O = 3 AMP + 3 diphosphate + N-[L-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine
For diagram of penicillin-N and deacetoxycephalosporin-C biosynthesis, click here and for possible mechanism of reaction, click here
Other name(s): L-δ-(α-aminoadipoyl)-L-cysteinyl-D-valine synthetase; ACV synthetase; L-α-aminoadipyl-cysteinyl-valine synthetase;
Systematic name: L-2-aminohexanedioate:L-cysteine:L-valine ligase (AMP-forming, valine-inverting)
Comments: Requires Mg2+. The enzyme contains 4′-phosphopantetheine, which may be involved in the mechanism of the reaction. Forms part of the penicillin biosynthesis pathway (for pathway, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 57219-73-5
References:
1.  Byford, M.F., Baldwin, J.E., Shiau, C.-Y. and Schofield, C.J. The mechanism of ACV synthetase. Chem. Rev. 97 (1997) 2631–2649. [DOI] [PMID: 11851475]
2.  Theilgaard, H.B., Kristiansen, K.N., Henriksen, C.M. and Nielsen, J. Purification and characterization of δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine synthetase from Penicillium chrysogenum. Biochem. J. 327 (1997) 185–191. [PMID: 9355751]
[EC 6.3.2.26 created 2002]
 
 
EC 1.2.1.70     Relevance: 48.5%
Accepted name: glutamyl-tRNA reductase
Reaction: L-glutamate 1-semialdehyde + NADP+ + tRNAGlu = L-glutamyl-tRNAGlu + NADPH + H+
For diagram of the early stages of porphyrin biosynthesis, click here
Systematic name: L-glutamate-semialdehyde:NADP+ oxidoreductase (L-glutamyl-tRNAGlu-forming)
Comments: This enzyme forms part of the pathway for the biosynthesis of 5-aminolevulinate from glutamate, known as the C5 pathway. The route shown in the diagram is used in most eubacteria, and in all archaebacteria, algae and plants. However, in the α-proteobacteria, EC 2.3.1.37, 5-aminolevulinate synthase, is used in an alternative route to produce the product 5-aminolevulinate from succinyl-CoA and glycine. This route is found in the mitochondria of fungi and animals, organelles that are considered to be derived from an endosymbiotic α-proteobacterium. Although higher plants do not possess EC 2.3.1.37, the protistan Euglena gracilis possesses both the C5 pathway and EC 2.3.1.37.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 119940-26-0
References:
1.  von Wettstein, D., Gough, S. and Kannangara, C.G. Chlorophyll biosynthesis. Plant Cell 7 (1995) 1039–1057. [DOI] [PMID: 12242396]
2.  Pontoppidan, B. and Kannangara, C.G. Purification and partial characterisation of barley glutamyl-tRNAGlu reductase, the enzyme that directs glutamate to chlorophyll biosynthesis. Eur. J. Biochem. 225 (1994) 529–537. [DOI] [PMID: 7957167]
3.  Schauer, S., Chaturvedi, S., Randau, L., Moser, J., Kitabatake, M., Lorenz, S., Verkamp, E., Schubert, W.D., Nakayashiki, T., Murai, M., Wall, K., Thomann, H.-U., Heinz, D.W., Inokuchi, H, Söll, D. and Jahn, D. Escherichia coli glutamyl-tRNA reductase. Trapping the thioester intermediate. J. Biol. Chem. 277 (2002) 48657–48663. [DOI] [PMID: 12370189]
[EC 1.2.1.70 created 2004]
 
 
EC 2.9.1.1     Relevance: 48.5%
Accepted name: L-seryl-tRNASec selenium transferase
Reaction: L-seryl-tRNASec + selenophosphate = L-selenocysteinyl-tRNASec + phosphate
Other name(s): L-selenocysteinyl-tRNASel synthase; L-selenocysteinyl-tRNASec synthase selenocysteine synthase; cysteinyl-tRNASec-selenium transferase; cysteinyl-tRNASec-selenium transferase
Systematic name: selenophosphate:L-seryl-tRNASec selenium transferase
Comments: A pyridoxal 5′-phosphate enzyme identified in Escherichia coli. Recognises specifically tRNASec-species. Binding of tRNASec also occurs in the absence of the seryl group. 2-Aminoacryloyl-tRNA, bound to the enzyme as an imine with the pyridoxal phosphate, is an intermediate in the reaction. Since the selenium atom replaces oxygen in serine, the product may also be referred to as L-selenoseryl-tRNASec. The symbol Sel has also been used for selenocysteine but Sec is preferred.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 183869-06-9
References:
1.  Forchhammer, K., Böck, A. Selenocysteine from Escherichia coli. Analysis of the reaction sequence. J. Biol. Chem. 266 (1991) 6324–6328. [PMID: 2007585]
[EC 2.9.1.1 created 1999]
 
 
EC 2.7.8.27     Relevance: 48.1%
Accepted name: sphingomyelin synthase
Reaction: a ceramide + a phosphatidylcholine = a sphingomyelin + a 1,2-diacyl-sn-glycerol
For diagram of reaction, click here
Glossary: sphingomyelin = a ceramide-1-phosphocholine
ceramide = an N-acylsphingoid. The fatty acids of naturally occurring ceramides range in chain length from about C16 to about C26 and may contain one or more double bonds and/or hydroxy substituents at C-2
sphingoid = sphinganine, i.e. D-erythro-2-aminooctadecane-1,3-diol, and its homologues and stereoisomers (see also Lip-1.4)
Other name(s): SM synthase; SMS1; SMS2
Systematic name: ceramide:phosphatidylcholine cholinephosphotransferase
Comments: The reaction can occur in both directions [3]. This enzyme occupies a central position in sphingolipid and glycerophospholipid metabolism [4]. Up- and down-regulation of its activity has been linked to mitogenic and pro-apoptotic signalling in a variety of mammalian cell types [4]. Unlike EC 2.7.8.3, ceramide cholinephosphotransferase, CDP-choline cannot replace phosphatidylcholine as the donor of the phosphocholine moiety of sphingomyelin [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 58703-97-2
References:
1.  Ullman, M.D. and Radin, N.S. The enzymatic formation of sphingomyelin from ceramide and lecithin in mouse liver. J. Biol. Chem. 249 (1974) 1506–1512. [PMID: 4817756]
2.  Voelker, D.R. and Kennedy, E.P. Cellular and enzymic synthesis of sphingomyelin. Biochemistry 21 (1982) 2753–2759. [PMID: 7093220]
3.  Huitema, K., van den Dikkenberg, J., Brouwers, J.F. and Holthuis, J.C. Identification of a family of animal sphingomyelin synthases. EMBO J. 23 (2004) 33–44. [DOI] [PMID: 14685263]
4.  Tafesse, F.G., Ternes, P. and Holthuis, J.C. The multigenic sphingomyelin synthase family. J. Biol. Chem. 281 (2006) 29421–29425. [DOI] [PMID: 16905542]
5.  Yamaoka, S., Miyaji, M., Kitano, T., Umehara, H. and Okazaki, T. Expression cloning of a human cDNA restoring sphingomyelin synthesis and cell growth in sphingomyelin synthase-defective lymphoid cells. J. Biol. Chem. 279 (2004) 18688–18693. [DOI] [PMID: 14976195]
[EC 2.7.8.27 created 2006]
 
 
EC 2.7.8.13     Relevance: 46.8%
Accepted name: phospho-N-acetylmuramoyl-pentapeptide-transferase
Reaction: UDP-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala) + undecaprenyl phosphate = UMP + Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol
Other name(s): MraY transferase; UDP-MurNAc-L-Ala-D-γ-Glu-L-Lys-D-Ala-D-Ala:C55-isoprenoid alcohol transferase; UDP-MurNAc-Ala-γDGlu-Lys-DAla-DAla:undecaprenylphosphate transferase; phospho-N-acetylmuramoyl pentapeptide translocase; phospho-MurNAc-pentapeptide transferase; phospho-NAc-muramoyl-pentapeptide translocase (UMP); phosphoacetylmuramoylpentapeptide translocase; phosphoacetylmuramoylpentapeptidetransferase
Systematic name: UDP-MurAc(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala):undecaprenyl-phosphate phospho-N-acetylmuramoyl-pentapeptide-transferase
Comments: In Gram-negative and some Gram-positive organisms the L-lysine is replaced by meso-2,6-diaminoheptanedioate (meso-2,6-diaminopimelate, A2pm), which is combined with adjacent residues through its L-centre. The undecaprenol involved is ditrans,octacis-undecaprenol (for definitions, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9068-50-2
References:
1.  Heydanek, M.G., Jr. and Neuhaus, F.C. The initial stage in peptidoglycan synthesis. IV. Solubilization of phospho-N-acetylmuramyl-pentapeptide translocase. Biochemistry 8 (1969) 1474–1481. [PMID: 5805290]
2.  Higashi, Y., Strominger, J.L. and Sweeley, C.C. Structure of a lipid intermediate in cell wall peptidoglycan synthesis: a derivative of a C55 isoprenoid alcohol. Proc. Natl. Acad. Sci. USA 57 (1967) 1878–1884. [DOI] [PMID: 5231417]
3.  Struve, W.G., Sinha, R.K. and Neuhaus, F.C. On the initial stage in peptidoglycan synthesis. Phospho-N-acetylmuramyl-pentapeptide translocase (uridine monophosphate). Biochemistry 5 (1966) 82–93. [PMID: 5938956]
4.  van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503–519. [PMID: 11699883]
[EC 2.7.8.13 created 1972, modified 2002]
 
 
EC 2.4.1.129     Relevance: 44.1%
Accepted name: peptidoglycan glycosyltransferase
Reaction: [GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)]n-diphosphoundecaprenol + GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = [GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)]n+1-diphosphoundecaprenol + undecaprenyl diphosphate
Glossary: Mur2Ac = N-acetylmuramic acid
Other name(s): PG-II; bactoprenyldiphospho-N-acetylmuramoyl-(N-acetyl-D-glucosaminyl)-pentapeptide:peptidoglycan N-acetylmuramoyl-N-acetyl-D-glucosaminyltransferase; penicillin binding protein (3 or 1B); peptidoglycan transglycosylase; undecaprenyldiphospho-(N-acetyl-D-glucosaminyl-(1→4)-N-acetyl-D-muramoylpentapeptide):undecaprenyldiphospho-(N-acetyl-D-glucosaminyl-(1→4)-N-acetyl-D-muramoylpentapeptide) disaccharidetransferase
Systematic name: [poly-N-acetyl-D-glucosaminyl-(1→4)-(N-acetyl-D-muramoylpentapeptide)]-diphosphoundecaprenol:[N-acetyl-D-glucosaminyl-(1→4)-N-acetyl-D-muramoylpentapeptide]-diphosphoundecaprenol disaccharidetransferase
Comments: The enzyme also works when the lysine residue is replaced by meso-2,6-diaminoheptanedioate (meso-2,6-diaminopimelate, A2pm) combined with adjacent residues through its L-centre, as it is in Gram-negative and some Gram-positive organisms. The undecaprenol involved is ditrans,octacis-undecaprenol (for definitions, click here). Involved in the synthesis of cell-wall peptidoglycan.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 79079-04-2
References:
1.  Taku, A., Stuckey, M. and Fan, D.P. Purification of the peptidoglycan transglycosylase of Bacillus megaterium. J. Biol. Chem. 257 (1982) 5018–5022. [PMID: 6802846]
2.  Goffin, C. and Ghuysen, J.-M. Multimodular penicillin-binding proteins: an enigmatic family of orthologs and paralogs. Microbiol. Mol. Biol. Rev. 62 (1998) 1079–1093. [PMID: 9841666]
3.  van Heijenoort, J. Formation of the glycan chains in the synthesis of bacterial peptidoglycan. Glycobiology 11 (2001) 25. [DOI] [PMID: 11320055]
[EC 2.4.1.129 created 1984, modified 2002]
 
 
EC 6.3.2.10     Relevance: 44%
Accepted name: UDP-N-acetylmuramoyl-tripeptide—D-alanyl-D-alanine ligase
Reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-L-lysine + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-L-lysyl-D-alanyl-D-alanine
Other name(s): MurF synthetase; UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine synthetase; UDP-N-acetylmuramoylalanyl-D-glutamyl-lysine-D-alanyl-D-alanine ligase; uridine diphosphoacetylmuramoylpentapeptide synthetase; UDPacetylmuramoylpentapeptide synthetase; UDP-MurNAc-L-Ala-D-Glu-L-Lys:D-Ala-D-Ala ligase
Systematic name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine:D-alanyl-D-alanine ligase (ADP-forming)
Comments: Involved with EC 6.3.2.4 (D-alanine—D-alanine ligase), EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase) or EC 6.3.2.13 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—2,6-diaminopimelate ligase), EC 6.3.2.8 (UDP-N-acetylmuramate—L-alanine ligase) and EC 6.3.2.9 (UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase) in the synthesis of a cell-wall peptide (click here) for diagram. This enzyme also catalyses the reaction when the C-terminal residue of the tripeptide is meso-2,4-diaminoheptanedioate (acylated at its L-centre), linking the D-Ala-D-Ala to the carboxy group of the L-centre. This activity was previously attributed to EC 6.3.2.15, which has since been deleted.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 55354-36-4
References:
1.  Ito, E. and Strominger, J.L. Enzymatic synthesis of the peptide in bacterial uridine nucleotides. II. Enzymatic synthesis and addition of D-alanyl-D-alanine. J. Biol. Chem. 237 (1962) 2696–2703.
2.  van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503–519. [PMID: 11699883]
[EC 6.3.2.10 created 1965, modified 2002]
 
 
EC 4.2.2.19     Relevance: 42.6%
Accepted name: chondroitin B lyase
Reaction: Eliminative cleavage of dermatan sulfate containing (1→4)-β-D-hexosaminyl and (1→3)-β-D-glucurosonyl or (1→3)-α-L-iduronosyl linkages to disaccharides containing 4-deoxy-β-D-gluc-4-enuronosyl groups to yield a 4,5-unsaturated dermatan-sulfate disaccharide (ΔUA-GalNAc-4S).
Glossary: chondroitin sulfate B = dermatan sulfate
For the nomenclature of glycoproteins, glycopeptides and peptidoglycans, click here
Other name(s): chondroitinase B; ChonB; ChnB
Systematic name: chondroitin B lyase
Comments: This is the only lyase that is known to be specific for dermatan sulfate as substrate. The minimum substrate length required for catalysis is a tetrasaccharide [2]. In general, chondroitin sulfate (CS) and dermatan sulfate (DS) chains comprise a linkage region, a chain cap and a repeat region. The repeat region of CS is a repeating disaccharide of glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc) [-4)GlcA(β1-3)GalNAc(β1-]n, which may be O-sulfated on the C-4 and/or C-6 of GalNAc and C-2 of GlcA. GlcA residues of CS may be epimerized to iduronic acid (IdoA) forming the repeating disaccharide [-4)IdoA(α1-3)GalNAc(β1-]n of DS. Both the concentrations and locations of sulfate-ester substituents vary with glucosaminoglycan source [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 52227-83-5
References:
1.  Gu, K., Linhardt, R.J., Laliberte, M., Gu, K. and Zimmermann, J. Purification, characterization and specificity of chondroitin lyases and glycuronidase from Flavobacterium heparinum. Biochem. J. 312 (1995) 569–577. [PMID: 8526872]
2.  Pojasek, K., Raman, R., Kiley, P., Venkataraman, G. and Sasisekharan, R. Biochemical characterization of the chondroitinase B active site. J. Biol. Chem. 277 (2000) 31179–31186. [DOI] [PMID: 12063249]
3.  Pojasek, K., Shriver, Z., Kiley, P., Venkataraman, G. and Sasisekharan, R. Recombinant expression, purification, and kinetic characterization of chondroitinase AC and chondroitinase B from Flavobacterium heparinum. Biochem. Biophys. Res. Commun. 286 (2001) 343–351. [DOI] [PMID: 11500043]
4.  Suzuki, K., Terasaki, Y. and Uyeda, M. Inhibition of hyaluronidases and chondroitinases by fatty acids. J. Enzyme 17 (2002) 183–186. [DOI] [PMID: 12443044]
5.  Ototani, N. and Yosizawa, Z. Purification of chondroitinase B and chondroitinase C using glycosaminoglycan-bound AH-Sepharose 4B. Carbohydr. Res. 70 (1979) 295–306. [DOI] [PMID: 427837]
6.  Tkalec, A.L., Fink, D., Blain, F., Zhang-Sun, G., Laliberte, M., Bennett, D.C., Gu, K., Zimmermann, J.J. and Su, H. Isolation and expression in Escherichia coli of cslA and cslB, genes coding for the chondroitin sulfate-degrading enzymes chondroitinase AC and chondroitinase B, respectively, from Flavobacterium heparinum. Appl. Environ. Microbiol. 66 (2000) 29–35. [DOI] [PMID: 10618199]
7.  Michel, G., Pojasek, K., Li, Y., Sulea, T., Linhardt, R.J., Raman, R., Prabhakar, V., Sasisekharan, R. and Cygler, M. The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery. J. Biol. Chem. 279 (2004) 32882–32896. [DOI] [PMID: 15155751]
8.  Li, Y., Matte, A., Su, H. and Cygler, M. Crystallization and preliminary X-ray analysis of chondroitinase B from Flavobacterium heparinum. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 1055–1057. [PMID: 10216304]
9.  Huang, W., Matte, A., Li, Y., Kim, Y.S., Linhardt, R.J., Su, H. and Cygler, M. Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 Å resolution. J. Mol. Biol. 294 (1999) 1257–1269. [DOI] [PMID: 10600383]
10.  Huckerby, T.N., Nieduszynski, I.A., Giannopoulos, M., Weeks, S.D., Sadler, I.H. and Lauder, R.M. Characterization of oligosaccharides from the chondroitin/dermatan sulfates. 1H-NMR and 13C-NMR studies of reduced trisaccharides and hexasaccharides. FEBS J. 272 (2005) 6276–6286. [DOI] [PMID: 16336265]
[EC 4.2.2.19 created 2005]
 
 
EC 4.2.2.21     Relevance: 42.3%
Accepted name: chondroitin-sulfate-ABC exolyase
Reaction: Exolytic removal of Δ4-unsaturated disaccharide residues from the non-reducing ends of both polymeric chondroitin/dermatan sulfates and their oligosaccharide fragments.
For diagram of reaction click here
Glossary: chondroitin sulfate A = chondroitin 4-sulfate
chondroitin sulfate B = dermatan sulfate
chondroitin sulfate C = chondroitin 6-sulfate
For the nomenclature of glycoproteins, glycopeptides and peptidoglycans, click here
Other name(s): chondroitinase (ambiguous); chondroitin ABC eliminase (ambiguous); chondroitinase ABC (ambiguous); chondroitin ABC lyase (ambiguous); chondroitin sulfate ABC lyase (ambiguous); ChS ABC lyase (ambiguous); chondroitin sulfate ABC exoeliminase; chondroitin sulfate ABC exolyase; ChS ABC lyase II
Systematic name: chondroitin-sulfate-ABC exolyase
Comments: This enzyme degrades a variety of glycosaminoglycans of the chondroitin-sulfate- and dermatan-sulfate type. Chondroitin sulfate, chondroitin-sulfate proteoglycan and dermatan sulfate are the best substrates but the enzyme can also act on hyaluronan at a much lower rate. Keratan sulfate, heparan sulfate and heparin are not substrates. The related enzyme EC 4.2.2.20, chondroitin-sulfate-ABC endolyase, has the same substrate specificity but produces a mixture of oligosaccharides of different sizes that are ultimately degraded to tetra- and disaccharides [4]. Both enzymes act by the removal of a relatively acidic C-5 proton of the uronic acid followed by the elimination of a 4-linked hexosamine, resulting in the formation of an unsaturated C4C5 bond on the hexuronic acid moiety of the products [4,6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 1000607-06-6
References:
1.  Yamagata, T., Saito, H., Habuchi, O. and Suzuki, S. Purification and properties of bacterial chondroitinases and chondrosulfatases. J. Biol. Chem. 243 (1968) 1523–1535. [PMID: 5647268]
2.  Saito, H., Yamagata, T. and Suzuki, S. Enzymatic methods for the determination of small quantities of isomeric chondroitin sulfates. J. Biol. Chem. 243 (1968) 1536–1542. [PMID: 4231029]
3.  Suzuki, S., Saito, H., Yamagata, T., Anno, K., Seno, N., Kawai, Y. and Furuhashi, T. Formation of three types of disulfated disaccharides from chondroitin sulfates by chondroitinase digestion. J. Biol. Chem. 243 (1968) 1543–1550. [PMID: 5647269]
4.  Hamai, A., Hashimoto, N., Mochizuki, H., Kato, F., Makiguchi, Y., Horie, K. and Suzuki, S. Two distinct chondroitin sulfate ABC lyases. An endoeliminase yielding tetrasaccharides and an exoeliminase preferentially acting on oligosaccharides. J. Biol. Chem. 272 (1997) 9123–9130. [DOI] [PMID: 9083041]
5.  Huckerby, T.N., Nieduszynski, I.A., Giannopoulos, M., Weeks, S.D., Sadler, I.H. and Lauder, R.M. Characterization of oligosaccharides from the chondroitin/dermatan sulfates. 1H-NMR and 13C-NMR studies of reduced trisaccharides and hexasaccharides. FEBS J. 272 (2005) 6276–6286. [DOI] [PMID: 16336265]
6.  Zhang, Z., Park, Y., Kemp, M.M., Zhao, W., Im, A.R., Shaya, D., Cygler, M., Kim, Y.S. and Linhardt, R.J. Liquid chromatography-mass spectrometry to study chondroitin lyase action pattern. Anal. Biochem. 385 (2009) 57–64. [DOI] [PMID: 18992215]
[EC 4.2.2.21 created 2006 (EC 4.2.2.4 created 1972, part-incorporated 2006 (EC 4.2.99.6 created 1965, part incorporated 1976)), modified 2010]
 
 
EC 2.4.1.243     Relevance: 41.8%
Accepted name: 6G-fructosyltransferase
Reaction: [1-β-D-fructofuranosyl-(2→1)-]m+1-α-D-glucopyranoside + [1-β-D-fructofuranosyl-(2→1)-]n-α-D-glucopyranoside = [1-β-D-fructofuranosyl-(2→1)-]m-α-D-glucopyranoside + [1-β-D-fructofuranosyl-(2→1)-]n-β-D-fructofuranosyl-(2→6)-α-D-glucopyranoside (m > 0; n ≥ 0)
Glossary: [1-β-D-fructofuranosyl-(2→1)-]n-α-D-glucopyranoside = inulin
Other name(s): fructan:fructan 6G-fructosyltransferase; 1F(1-β-D-fructofuranosyl)m sucrose:1F(1-β-D-fructofuranosyl)nsucrose 6G-fructosyltransferase; 6G-FFT; 6G-FT; 6G-fructotransferase
Systematic name: 1F-oligo[β-D-fructofuranosyl-(2→1)-]sucrose 6G-β-D-fructotransferase
Comments: Inulins are polysaccharides consisting of linear or branched D-fructofuranosyl chains attached to the fructosyl residue of sucrose by a β(2→1) linkage. This enzyme catalyses the transfer of the terminal (2→1)-linked -D-fructosyl group of an inulin chain onto O-6 position of the glucose residue of another inulin molecule [1]. For example, if 1-kestose [1F-(β-D-fructofuranosyl)sucrose] is both the donor and recipient in the reaction shown above, i.e., if m = 1 and n = 1, then the products will be sucrose and 6G-di-β-D-fructofuranosylsucrose. In this notation, the superscripts F and G are used to specify whether the fructose or glucose residue of the sucrose carries the substituent. Alternatively, this may be indicated by the presence and/or absence of primes (see http://www.chem.qmul.ac.uk/iupac/2carb/36.html#362). Sucrose cannot be a donor substrate in the reaction (i.e. m cannot be zero) and inulin cannot act as an acceptor. Side reactions catalysed are transfer of a β-D-fructosyl group between compounds of the structure 1F-(1-β-D-fructofuranosyl)m-6G-(1-β-D-fructofuranosyl)n sucrose, where m ≥ 0 and n = 1 for the donor, and m ≥ 0 and n ≥ 0 for the acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 79633-28-6
References:
1.  Shiomi, N. Purification and characterisation of 6G-fructosyltransferase from the roots of asparagus (Asparagus officinalis L.). Carbohydr. Res. 96 (1981) 281–292.
2.  Shiomi, N. Reverse reaction of fructosyl transfer catalysed by asparagus 6G-fructosyltransferase. Carbohydr. Res. 106 (1982) 166–169.
3.  Shiomi, N. and Ueno, K. Cloning and expression of genes encoding fructosyltransferases from higher plants in food technology. J. Appl. Glycosci. 51 (2004) 177–183.
4.  Ueno, K., Onodera, S., Kawakami, A., Yoshida, M. and Shiomi, N. Molecular characterization and expression of a cDNA encoding fructan:fructan 6G-fructosyltransferase from asparagus (Asparagus officinalis). New Phytol. 165 (2005) 813–824. [DOI] [PMID: 15720693]
[EC 2.4.1.243 created 2006]
 
 
EC 2.7.1.156     Relevance: 39%
Accepted name: adenosylcobinamide kinase
Reaction: RTP + adenosylcobinamide = adenosylcobinamide phosphate + RDP [where RTP is either ATP or GTP (for symbol definitions, click here)]
For diagram of the enzyme’s role in corrin biosynthesis, click here
Other name(s): CobU; adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; AdoCbi kinase/AdoCbi-phosphate guanylyltransferase
Systematic name: RTP:adenosylcobinamide phosphotransferase
Comments: In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT (EC 2.4.2.21), CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop assembly pathway, which convert adenosylcobinamide (AdoCbi) into adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby 5,6-dimethylbenzimidazole is converted to its riboside, α-ribazole. The second branch of the nucleotide loop assembly pathway is the cobinamide (Cbi) activation branch where AdoCbi or adenosylcobinamide-phosphate is converted to the activated intermediate AdoCbi-GDP by Cob U. The final step in adenosylcobalamin biosynthesis is the condensation of AdoCbi-GDP with α-ribazole, which is catalysed by EC 2.7.8.26, adenosylcobinamide-GDP ribazoletransferase (CobS), to yield adenosylcobalamin. CobU is a bifunctional enzyme that has both kinase (EC 2.7.1.156) and guanylyltransferase (EC 2.7.7.62, adenosylcobinamide-phosphate guanylyltransferase) activities. However, both activities are not required at all times. The kinase activity has been proposed to function only when S. typhimurium is assimilating cobinamide whereas the guanylyltransferase activity is required for both assimilation of exogenous cobinamide and for de novo synthesis of adenosylcobalamin [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 169592-51-2
References:
1.  O'Toole, G.A. and Escalante-Semerena, J.C. Purification and characterization of the bifunctional CobU enzyme of Salmonella typhimurium LT2. Evidence for a CobU-GMP intermediate. J. Biol. Chem. 270 (1995) 23560–23569. [DOI] [PMID: 7559521]
2.  Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 Å resolution. Biochemistry 37 (1998) 7686–7695. [DOI] [PMID: 9601028]
3.  Thompson, T.B., Thomas, M.G., Escalante-Semerena, J.C. and Rayment, I. Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site. Biochemistry 38 (1999) 12995–13005. [DOI] [PMID: 10529169]
4.  Thomas, M.G., Thompson, T.B., Rayment, I. and Escalante-Semerena, J.C. Analysis of the adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue His-46 as the site of guanylylation. J. Biol. Chem. 275 (2000) 27576–27586. [DOI] [PMID: 10869342]
5.  Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390–412. [PMID: 12195810]
[EC 2.7.1.156 created 2004]
 
 
EC 1.11.1.15     Relevance: 37.9%
Accepted name: peroxiredoxin
Reaction: 2 R′-SH + ROOH = R′-S-S-R′ + H2O + ROH
For diagram of reaction, click here and for mechanism, click here
Other name(s): thioredoxin peroxidase; tryparedoxin peroxidase; alkyl hydroperoxide reductase C22; AhpC; TrxPx; TXNPx; Prx; PRDX
Systematic name: thiol-containing-reductant:hydroperoxide oxidoreductase
Comments: Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [1]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ’resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants (R′-SH) (e.g. thioredoxin, AhpF, tryparedoxin or AhpD), completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond [1]. To recycle the disulfide, known atypical 2-Cys Prxs appear to use thioredoxin as an electron donor [3]. The 1-Cys Prxs conserve only the peroxidatic cysteine, so that its oxidized form is directly reduced to cysteine by the reductant molecule [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 207137-51-7
References:
1.  Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
2.  Hofmann, B., Hecht, H.J. and Flohé, L. Peroxiredoxins. Biol. Chem. 383 (2002) 347–364. [DOI] [PMID: 12033427]
3.  Seo, M.S., Kang, S.W., Kim, K., Baines, I.C., Lee, T.H. and Rhee, S.G. Identification of a new type of mammalian peroxiredoxin that forms an intramolecular disulfide as a reaction intermediate. J. Biol. Chem. 275 (2000) 20346–20354. [DOI] [PMID: 10751410]
4.  Choi, H.J., Kang, S.W., Yang, C.H., Rhee, S.G. and Ryu, S.E. Crystal structure of a novel human peroxidase enzyme at 2.0 Å resolution. Nat. Struct. Biol. 5 (1998) 400–406. [PMID: 9587003]
[EC 1.11.1.15 created 2004]
 
 
EC 4.2.2.20     Relevance: 35.7%
Accepted name: chondroitin-sulfate-ABC endolyase
Reaction: Endolytic cleavage of (1→4)-β-galactosaminic bonds between N-acetylgalactosamine and either D-glucuronic acid or L-iduronic acid to produce a mixture of Δ4-unsaturated oligosaccharides of different sizes that are ultimately degraded to Δ4-unsaturated tetra- and disaccharides
For diagram of reaction click here
Glossary: chondroitin sulfate A = chondroitin 4-sulfate
chondroitin sulfate B = dermatan sulfate
chondroitin sulfate C = chondroitin 6-sulfate
For the nomenclature of glycoproteins, glycopeptides and peptidoglycans, click here
Other name(s): chondroitinase (ambiguous); chondroitin ABC eliminase (ambiguous); chondroitinase ABC (ambiguous); chondroitin ABC lyase (ambiguous); chondroitin sulfate ABC lyase (ambiguous); ChS ABC lyase (ambiguous); chondroitin sulfate ABC endoeliminase; chondroitin sulfate ABC endolyase; ChS ABC lyase I
Systematic name: chondroitin-sulfate-ABC endolyase
Comments: This enzyme degrades a variety of glycosaminoglycans of the chondroitin-sulfate- and dermatan-sulfate type. Chondroitin sulfate, chondroitin-sulfate proteoglycan and dermatan sulfate are the best substrates but the enzyme can also act on hyaluronan at a much lower rate. Keratan sulfate, heparan sulfate and heparin are not substrates. In general, chondroitin sulfate (CS) and dermatan sulfate (DS) chains comprise a linkage region, a chain cap and a repeat region. The repeat region of CS is a repeating disaccharide of glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc) [-4)GlcA(β1-3)GalNAc(β1-]n, which may be O-sulfated on the C-4 and/or C-6 of GalNAc and C-2 of GlcA. GlcA residues of CS may be epimerized to iduronic acid (IdoA) forming the repeating disaccharide [-4)IdoA(α1-3)GalNAc(β1-]n of DS. Both the concentrations and locations of sulfate-ester substituents vary with glucosaminoglycan source [5]. The related enzyme EC 4.2.2.21, chondroitin-sulfate-ABC exolyase, has the same substrate specificity but removes disaccharide residues from the non-reducing ends of both polymeric chondroitin sulfates and their oligosaccharide fragments produced by EC 4.2.2.20 [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-13-9
References:
1.  Yamagata, T., Saito, H., Habuchi, O. and Suzuki, S. Purification and properties of bacterial chondroitinases and chondrosulfatases. J. Biol. Chem. 243 (1968) 1523–1535. [PMID: 5647268]
2.  Saito, H., Yamagata, T. and Suzuki, S. Enzymatic methods for the determination of small quantities of isomeric chondroitin sulfates. J. Biol. Chem. 243 (1968) 1536–1542. [PMID: 4231029]
3.  Suzuki, S., Saito, H., Yamagata, T., Anno, K., Seno, N., Kawai, Y. and Furuhashi, T. Formation of three types of disulfated disaccharides from chondroitin sulfates by chondroitinase digestion. J. Biol. Chem. 243 (1968) 1543–1550. [PMID: 5647269]
4.  Hamai, A., Hashimoto, N., Mochizuki, H., Kato, F., Makiguchi, Y., Horie, K. and Suzuki, S. Two distinct chondroitin sulfate ABC lyases. An endoeliminase yielding tetrasaccharides and an exoeliminase preferentially acting on oligosaccharides. J. Biol. Chem. 272 (1997) 9123–9130. [DOI] [PMID: 9083041]
5.  Huckerby, T.N., Nieduszynski, I.A., Giannopoulos, M., Weeks, S.D., Sadler, I.H. and Lauder, R.M. Characterization of oligosaccharides from the chondroitin/dermatan sulfates. 1H-NMR and 13C-NMR studies of reduced trisaccharides and hexasaccharides. FEBS J. 272 (2005) 6276–6286. [DOI] [PMID: 16336265]
[EC 4.2.2.20 created 2006 (EC 4.2.2.4 created 1972, part-incorporated 2006 (EC 4.2.99.6 created 1965, part incorporated 1976))]
 
 


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