The Enzyme Database

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

EC 1.3.1.59 deleted
EC 1.4.3.20 L-lysine 6-oxidase
*EC 2.1.1.69 5-hydroxyfuranocoumarin 5-O-methyltransferase
*EC 2.1.1.70 8-hydroxyfuranocoumarin 8-O-methyltransferase
EC 2.1.1.92 deleted
EC 3.4.14.12 Xaa-Xaa-Pro tripeptidyl-peptidase
EC 3.4.21.107 peptidase Do
EC 3.4.21.111 aqualysin 1
EC 3.4.21.113 pestivirus NS3 polyprotein peptidase
EC 3.4.21.116 SpoIVB peptidase
*EC 4.1.2.8 indole-3-glycerol-phosphate lyase


EC 1.3.1.59
Deleted entry: 1,2-dihydroxy-3-methyl-1,2-dihydrobenzoate dehydrogenase. No evidence in the paper cited that the enzyme exists
[EC 1.3.1.59 created 2000, deleted 2006]
 
 
EC 1.4.3.20
Accepted name: L-lysine 6-oxidase
Reaction: L-lysine + O2 + H2O = (S)-2-amino-6-oxohexanoate + H2O2 + NH3
Glossary: (S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine
Other name(s): L-lysine-ε-oxidase; Lod; LodA; marinocine
Systematic name: L-lysine:oxygen 6-oxidoreductase (deaminating)
Comments: Differs from EC 1.4.3.13, protein-lysine 6-oxidase, by using free L-lysine rather than the protein-bound form. N2-Acetyl-L-lysine is also a substrate, but N6-acetyl-L-lysine, which has an acetyl group at position 6, is not a substrate. Also acts on L-ornithine, D-lysine and 4-hydroxy-L-lysine, but more slowly. The amines cadaverine and putrescine are not substrates [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 1116448-48-6
References:
1.  Lucas-Elío, P., Gómez, D., Solano, F. and Sanchez-Amat, A. The antimicrobial activity of marinocine, synthesized by Marinomonas mediterranea, is due to hydrogen peroxide generated by its lysine oxidase activity. J. Bacteriol. 188 (2006) 2493–2501. [PMID: 16547036]
2.  Gómez, D., Lucas-Elío, P., Sanchez-Amat, A. and Solano, F. A novel type of lysine oxidase: L-lysine-ε-oxidase. Biochim. Biophys. Acta 1764 (2006) 1577–1585. [PMID: 17030025]
[EC 1.4.3.20 created 2006, modified 2011]
 
 
*EC 2.1.1.69
Accepted name: 5-hydroxyfuranocoumarin 5-O-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + a 5-hydroxyfurocoumarin = S-adenosyl-L-homocysteine + a 5-methoxyfurocoumarin (general reaction)
(2) S-adenosyl-L-methionine + bergaptol = S-adenosyl-L-homocysteine + bergapten
For diagram of reaction, click here
Glossary: bergaptol = 5-hydroxypsoralen
O-methylbergaptol = bergapten = 5-methoxypsoralen
Other name(s): furanocoumarin 5-methyltransferase; furanocoumarin 5-O-methyltransferase; bergaptol 5-O-methyltransferase; bergaptol O-methyltransferase; bergaptol methyltransferase; S-adenosyl-L-methionine:bergaptol O-methyltransferase; BMT; S-adenosyl-L-methionine:5-hydroxyfuranocoumarin 5-O-methyltransferase
Systematic name: S-adenosyl-L-methionine:5-hydroxyfurocoumarin 5-O-methyltransferase
Comments: Converts bergaptol into bergapten, which has therapeutic potential in the treatment of psoriasis as it has photosensitizing and antiproliferative activities [4]. The enzyme methylates the 5-hydroxy group of some hydroxy- and methylcoumarins, such as 5-hydroxyxanthotoxin [3], but has little activity on non-coumarin phenols [1]. Caffeate, 5-hydroxyferulate and daphnetin are not substrates [4]. Cu2+, Zn2+ and Co2+ cause enzyme inhibition [4]. (see also EC 2.1.1.70, 8-hydroxyfuranocoumarin 8-O-methyltransferase)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 67339-12-2, 101637-31-4
References:
1.  Thompson, H.J., Sharma, S.K. and Brown, S.A. O-Methyltransferases of furanocoumarin biosynthesis. Arch. Biochem. Biophys. 188 (1978) 272–281. [PMID: 28084]
2.  Sharma, S.K., Garrett, J.M. and Brown, S.A. Separation of the S-adenosylmethionine: 5- and 8-hydroxyfuranocoumarin O-methyltransferases of Ruta graveolens L. by general ligand affinity chromatography. Z. Naturforsch. [C] 34C (1979) 387–391. [PMID: 156999]
3.  Hauffe, K.D., Hahlbrock, K. and Scheel, D. Elicitor-stimulated furanocoumarin biosynthesis in cultured parsley cells - S-adenosyl-L-methionine-bergaptol and S-adenosyl-L-methionine-xanthotoxol O-methyltransferases. Z. Naturforsch. C: Biosci. 41 (1986) 228–239.
4.  Hehmann, M., Lukačin, R., Ekiert, H. and Matern, U. Furanocoumarin biosynthesis in Ammi majus L. Cloning of bergaptol O-methyltransferase. Eur. J. Biochem. 271 (2004) 932–940. [PMID: 15009205]
[EC 2.1.1.69 created 1984 (EC 2.1.1.92 created 1989, incorporated 2006), modified 2006]
 
 
*EC 2.1.1.70
Accepted name: 8-hydroxyfuranocoumarin 8-O-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + an 8-hydroxyfurocoumarin = S-adenosyl-L-homocysteine + an 8-methoxyfurocoumarin (general reaction)
(2) S-adenosyl-L-methionine + xanthotoxol = S-adenosyl-L-homocysteine + xanthotoxin
For diagram of reaction, click here
Glossary: xanthotoxin = O-methylxanthotoxol = 8-methoxypsoralen
xanthotoxol = 8-hydroxypsoralen
Other name(s): furanocoumarin 8-methyltransferase; furanocoumarin 8-O-methyl-transferase; xanthotoxol 8-O-methyltransferase; XMT; 8-hydroxyfuranocoumarin 8-O-methyltransferase; SAM:xanthotoxol O-methyltransferase; S-adenosyl-L-methionine:8-hydroxyfuranocoumarin 8-O-methyltransferase; xanthotoxol methyltransferase; xanthotoxol O-methyltransferase; S-adenosyl-L-methionine:xanthotoxol O-methyltransferase; S-adenosyl-L-methionine-xanthotoxol O-methyltransferase
Systematic name: S-adenosyl-L-methionine:8-hydroxyfurocoumarin 8-O-methyltransferase
Comments: Converts xanthotoxol into xanthotoxin, which has therapeutic potential in the treatment of psoriasis as it has photosensitizing and antiproliferative activities [4]. Methylates the 8-hydroxy group of some hydroxy- and methylcoumarins, but has little activity on non-coumarin phenols (see also EC 2.1.1.69, 5-hydroxyfuranocoumarin 5-O-methyltransferase).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 67339-13-3
References:
1.  Thompson, H.J., Sharma, S.K. and Brown, S.A. O-Methyltransferases of furanocoumarin biosynthesis. Arch. Biochem. Biophys. 188 (1978) 272–281. [PMID: 28084]
2.  Hauffe, K.D., Hahlbrock, K. and Scheel, D. Elicitor-stimulated furanocoumarin biosynthesis in cultured parsley cells - S-adenosyl-L-methionine-bergaptol and S-adenosyl-L-methionine-xanthotoxol O-methyltransferases. Z. Naturforsch. C: Biosci. 41 (1986) 228–239.
3.  Sharma, S.K., Garrett, J.M. and Brown, S.A. Separation of the S-adenosylmethionine: 5- and 8-hydroxyfuranocoumarin O-methyltransferases of Ruta graveolens L. by general ligand affinity chromatography. Z. Naturforsch. [C] 34C (1979) 387–391. [PMID: 156999]
4.  Hehmann, M., Lukačin, R., Ekiert, H. and Matern, U. Furanocoumarin biosynthesis in Ammi majus L. Cloning of bergaptol O-methyltransferase. Eur. J. Biochem. 271 (2004) 932–940. [PMID: 15009205]
[EC 2.1.1.70 created 1984, modified 2006 (EC 2.1.1.93 created 2006, incorporated 2008)]
 
 
EC 2.1.1.92
Deleted entry: bergaptol O-methyltransferase. Now included with EC 2.1.1.69, 5-hydroxyfuranocoumarin 5-O-methyltransferase. The reaction with bergaptol is a specific example of the general reaction associated with EC 2.1.1.69
[EC 2.1.1.92 created 1989, deleted 2006]
 
 
EC 3.4.14.12
Accepted name: Xaa-Xaa-Pro tripeptidyl-peptidase
Reaction: Hydrolysis of Xaa-Xaa-Pro┼Yaa- releasing the N-terminal tripeptide of a peptide with Pro as the third residue (position P1) and where Yaa is not proline
Other name(s): prolyltripeptidyl amino peptidase; prolyl tripeptidyl peptidase; prolyltripeptidyl aminopeptidase; PTP-A; TPP
Comments: This cell-surface-associated serine exopeptidase is found in the Gram-negative, anaerobic bacterium Porphyromonas gingivalis, which has been implicated in adult periodontal disease [1]. The enzyme releases the N-terminal tripeptide of peptides, such as interleukin-6. It has an absolute requirement for a proline residue at the P1 position but is completely inactivated by a proline residue at the P1′ position [1]. The size of the peptide does not affect the rate of reaction [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Banbula, A., Mak, P., Bugno, M., Silberring, J., Dubin, A., Nelson, D., Travis, J. and Potempa, J. Prolyl tripeptidyl peptidase from Porphyromonas gingivalis. A novel enzyme with possible pathological implications for the development of periodontitis. J. Biol. Chem. 274 (1999) 9246–9252. [PMID: 10092598]
2.  Fujimura, S., Ueda, O., Shibata, Y. and Hirai, K. Isolation and properties of a tripeptidyl peptidase from a periodontal pathogen Prevotella nigrescens. FEMS Microbiol. Lett. 219 (2003) 305–309. [PMID: 12620636]
[EC 3.4.14.12 created 2006]
 
 
EC 3.4.21.107
Accepted name: peptidase Do
Reaction: Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val┼Val
Other name(s): DegP; DegP protease; HtrA; high temperature requirement protease A; HrtA heat shock protein; protease Do; Do protease
Comments: This serine endopeptidase is essential for the clearance of denatured or aggregated proteins from the inner-membrane and periplasmic space in Escherichia coli. Natural substrates of the enzyme include colicin A lysis protein, pilin subunits and MalS from E. coli [3]. The enzyme has weak peptidase activity with casein and other non-native substrates [3]. The peptidase acts as a chaperone at low temperatures but switches to a peptidase (heat shock protein) at higher temperatures [1,6]. Molecular chaperones and peptidases control the folded state of proteins by recognizing hydrophobic stretches of polypeptide that become exposed by misfolding or unfolding. They then bind these hydrophobic substrates to prevent aggregation or assist in protein refolding. If attempts at refolding fail, then irreversibly damaged proteins are degraded by peptidases such as this enzyme [6]. Belongs in peptidase family S1C.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 161108-11-8
References:
1.  Lipinska, B., Zylicz, M. and Georgopoulos, C. The HtrA (DegP) protein, essential for Escherichia coli survival at high temperatures, is an endopeptidase. J. Bacteriol. 172 (1990) 1791–1797. [PMID: 2180903]
2.  Seol, J.H., Woo, S.K., Jung, E.M., Yoo, S.J., Lee, C.S., Kim, K.J., Tanaka, K., Ichihara, A., Ha, D.B. and Chung, C.H. Protease Do is essential for survival of Escherichia coli at high temperatures: its identity with the htrA gene product. Biochem. Biophys. Res. Commun. 176 (1991) 730–736. [PMID: 2025286]
3.  Jones, C.H., Dexter, P., Evans, A.K., Liu, C., Hultgren, S.J. and Hruby, D.E. Escherichia coli DegP protease cleaves between paired hydrophobic residues in a natural substrate: the PapA pilin. J. Bacteriol. 184 (2002) 5762–5771. [PMID: 12270835]
4.  Swamy, K.H., Chung, C.H. and Goldberg, A.L. Isolation and characterization of protease Do from Escherichia coli, a large serine protease containing multiple subunits. Arch. Biochem. Biophys. 224 (1983) 543–554. [PMID: 6347072]
5.  Pallen, M.J. and Wren, B.W. The HtrA family of serine proteases. Mol. Microbiol. 26 (1997) 209–221. [PMID: 9383148]
6.  Krojer, T., Garrido-Franco, M., Huber, R., Ehrmann, M. and Clausen, T. Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine. Nature 416 (2002) 455–459. [PMID: 11919638]
[EC 3.4.21.107 created 2006]
 
 
EC 3.4.21.111
Accepted name: aqualysin 1
Reaction: Exhibits low specificity towards esters of amino acids with small hydrophobic or aromatic residues at the P1 position
Other name(s): caldolysin
Comments: This enzyme from the extreme thermophile, Thermus aquaticus, is an alkaline serine peptidase. It has three subsites, S1, S2, and S3, in the substrate binding site. The preferred amino acids at the S1 site are Ala and Phe, at the S2 site are Ala and norleucine and at the S3 site are Phe and Ile [3]. These specificities are similar to those of EC 3.4.21.64 (peptidase K) and EC 3.4.21.62 (subtilisin BPN′) [3]. The enzyme displays broad specificity for cleavage of insulin B-chain and hydrolyses elastin substrates such as succinyl-(Ala)n-p-nitroanilide (n = 1,2,3) and some peptide esters [1,3]. Belongs in peptidase family S8A.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 88747-68-6
References:
1.  Matsuzawa, H., Tokugawa, K., Hamaoki, M., Mizoguchi, M., Taguchi, H., Terada, I., Kwon, S.T. and Ohta, T. Purification and characterization of aqualysin I (a thermophilic alkaline serine protease) produced by Thermus aquaticus YT-1. Eur. J. Biochem. 171 (1988) 441–447. [PMID: 3162211]
2.  Tanaka, T., Matsuzawa, H., Kojima, S., Kumagai, I., Miura, K. and Ohta, T. P1 specificity of aqualysin I (a subtilisin-type serine protease) from Thermus aquaticus YT-1, using P1-substituted derivatives of Streptomyces subtilisin inhibitor. Biosci. Biotechnol. Biochem. 62 (1998) 2035–2038. [PMID: 9882104]
3.  Tanaka, T., Matsuzawa, H. and Ohta, T. Substrate specificity of aqualysin I, a bacterial thermophilic alkaline serine protease from Thermus aquaticus YT-1: Comparison with proteinase K, subtilisin BPN′ and subtilisin Carlsberg. Biosci. Biotechnol. Biochem. 62 (1998) 2161–2165.
[EC 3.4.21.111 created 2006]
 
 
EC 3.4.21.113
Accepted name: pestivirus NS3 polyprotein peptidase
Reaction: Leu is conserved at position P1 for all four cleavage sites. Alanine is found at position P1′ of the NS4A-NS4B cleavage site, whereas serine is found at position P1′ of the NS3-NS4A, NS4B-NS5A and NS5A-NS5B cleavage sites
Other name(s): border disease virus NS3 endopeptidase; BDV NS3 endopeptidase; bovine viral diarrhea virus NS3 endopeptidase; BVDV NS3 endopeptidase; classical swine fever virus NS3 endopeptidase; CSFV NS3 endopeptidase; p80
Comments: The polyprotein of noncytopathogenic pestiviruses is cleaved co- and post-translationally into at least 11 proteins (Npro, C, Erns, E1, E2, p7, NS2-3, NS4A, NS4B, NS5A, and NS5B) [2]. The genomes of cytopathogenic pestivirus strains express at least one additional protein, called NS3 (p80) [2]. This enzyme, which resides in the N-terminal region of NS3 (nonstructural protein 3), is essential for generation of its own C-terminus and for processing of the downstream cleavage sites, leading to the release of the pestivirus nonstructural proteins NS4A, NS4B, NS5A and NS5B [1,2]. Belongs in peptidase family S31.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Wiskerchen, M. and Collett, M.S. Pestivirus gene expression: protein p80 of bovine viral diarrhea virus is a proteinase involved in polyprotein processing. Virology 184 (1991) 341–350. [PMID: 1651596]
2.  Tautz, N., Elbers, K., Stoll, D., Meyers, G. and Thiel, H.J. Serine protease of pestiviruses: determination of cleavage sites. J. Virol. 71 (1997) 5415–5422. [PMID: 9188613]
3.  Xu, J., Mendez, E., Caron, P.R., Lin, C., Murcko, M.A., Collett, M.S. and Rice, C.M. Bovine viral diarrhea virus NS3 serine proteinase: polyprotein cleavage sites, cofactor requirements, and molecular model of an enzyme essential for pestivirus replication. J. Virol. 71 (1997) 5312–5322. [PMID: 9188600]
4.  Tautz, N., Kaiser, A. and Thiel, H.J. NS3 serine protease of bovine viral diarrhea virus: characterization of active site residues, NS4A cofactor domain, and protease-cofactor interactions. Virology 273 (2000) 351–363. [PMID: 10915606]
[EC 3.4.21.113 created 2006]
 
 
EC 3.4.21.116
Accepted name: SpoIVB peptidase
Reaction: Self-cleaves Val52┼Asn53, Ala62┼Phe63 and Val74┼Thr75 at the N-terminus of SpoIVB
Other name(s): sporulation factor IV B protease
Comments: This enzyme plays a central role in a regulatory checkpoint (the σK checkpoint), which coordinates gene expression during the later stages of spore formation in Bacillus subtilis [1,3]. The enzyme activates proteolytic processing of a sporulation-specific sigma factor, pro-σK, to its mature and active form, σK, by self-cleavage [1,3]. The enzyme is also subject to secondary proteolysis, which presumably inactivates SpoIVB [3]. The enzyme is also essential for the formation of heat-resistant spores. Belongs in peptidase family S55.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 296241-18-4
References:
1.  Wakeley, P.R., Dorazi, R., Hoa, N.T., Bowyer, J.R. and Cutting, S.M. Proteolysis of SpolVB is a critical determinant in signalling of pro-σK processing in Bacillus subtilis. Mol. Microbiol. 36 (2000) 1336–1348. [PMID: 10931284]
2.  Hoa, N.T., Brannigan, J.A. and Cutting, S.M. The PDZ domain of the SpoIVB serine peptidase facilitates multiple functions. J. Bacteriol. 183 (2001) 4364–4373. [PMID: 11418578]
3.  Hoa, N.T., Brannigan, J.A. and Cutting, S.M. The Bacillus subtilis signaling protein SpoIVB defines a new family of serine peptidases. J. Bacteriol. 184 (2002) 191–199. [PMID: 11741860]
4.  Dong, T.C. and Cutting, S.M. SpoIVB-mediated cleavage of SpoIVFA could provide the intercellular signal to activate processing of pro-σK in Bacillus subtilis. Mol. Microbiol. 49 (2003) 1425–1434. [PMID: 12940997]
[EC 3.4.21.116 created 2006]
 
 
*EC 4.1.2.8
Accepted name: indole-3-glycerol-phosphate lyase
Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
For diagram of reaction, click here
Other name(s): tryptophan synthase α; TSA; indoleglycerolphosphate aldolase; indole glycerol phosphate hydrolase; indole synthase; indole-3-glycerolphosphate D-glyceraldehyde-3-phosphate-lyase; indole-3-glycerol phosphate lyase; IGL; BX1; (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate D-glyceraldehyde-3-phosphate-lyase
Systematic name: (1S,2R)-1-C-(indol-3-yl)glycerol-3-phosphate D-glyceraldehyde-3-phosphate-lyase (indole-forming)
Comments: Forms part of the defence mechanism against insects and microbial pathogens in the grass family, Gramineae, where it catalyses the first committed step in the formation of the cyclic hydroxamic acids 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) [1]. This enzyme resembles the α-subunit of EC 4.2.1.20, tryptophan synthase [3], for which, (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate is also a substrate, but, unlike tryptophan synthase, its activity is independent of the β-subunit and free indole is released [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9014-52-2
References:
1.  Yanofsky, C. The enzymatic conversion of anthranilic acid to indole. J. Biol. Chem. 223 (1956) 171–184. [PMID: 13376586]
2.  Frey, M., Chomet, P., Glawischnig, E., Stettner, C., Grün, S., Winklmair, A., Eisenreich, W., Bacher, A., Meeley, R.B., Briggs, S.P., Simcox, K. and Gierl, A. Analysis of a chemical plant defense mechanism in grasses. Science 277 (1997) 696–699. [PMID: 9235894]
3.  Frey, M., Stettner, C., Paré, P.W., Schmelz, E.A., Tumlinson, J.H. and Gierl, A. An herbivore elicitor activates the gene for indole emission in maize. Proc. Natl. Acad. Sci. USA 97 (2000) 14801–14806. [PMID: 11106389]
4.  Melanson, D., Chilton, M.D., Masters-Moore, D. and Chilton, W.S. A deletion in an indole synthase gene is responsible for the DIMBOA-deficient phenotype of bxbx maize. Proc. Natl. Acad. Sci. USA 94 (1997) 13345–13350. [PMID: 9371848]
[EC 4.1.2.8 created 1961, deleted 1972, reinstated 2006]
 
 


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