An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Common name: polyneuridine-aldehyde esterase
Reaction: polyneuridine aldehyde + H2O = + 16-epivellosimine + CO2 + methanol
For diagram click here.
Other name(s): polyneuridine aldehyde esterase
Systematic name: polyneuridine aldehyde hydrolase (decarboxylating)
Comments: Following hydrolysis of this indole alkaloid ester the carboxylic acid decarboxylates spontaneously giving the sarpagan skeleton. The enzyme also acts on akuammidine aldehyde (the 16-epimer of polyneuridine aldehyde).
References:
1. Pfitzner, A. and Stöckigt, J. Characterization of polyneuridine aldehyde esterase, a key enzyme in the biosynthesis of sarpagine ajmaline type alkaloids. Planta Medica 48 (1983) 221-227.
2. Pfitzner, A. and Stöckigt, J. Polyneuridine aldehyde esterase: an unusual specific enzyme involved in the biosynthesis of sarpagine type alkaloids. J. Chem. Soc. Chem. Commun. (1983) 459-460.
3. Dogru, E., Warzecha, H., Seibel, F., Haebel, S., Lottspeich, F. and Stöckigt, J. The gene encoding polyneuridine aldehyde esterase of monoterpenoid indole alkaloid biosynthesis in plants is an ortholog of the α/βhydrolase super family. Eur. J. Biochem. 267 (2000) 1397-1406. [PMID: 10691977]
Common name: 3-phytase
Reaction: myo-inositol hexakisphosphate + H2O = 1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate
Other name(s): 1-phytase; phytase; phytate 1-phosphatase; phytate 6-phosphatase
Systematic name: myo-inositol-hexakisphosphate 3-phosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 37288-11-2
References:
1. Cosgrove, D.J. Ion-exchange chromatography of inositol polyphosphates. Ann. N.Y. Acad. Sci. 165 (1969) 677-686. [PMID: 4310381]
2. Johnson, L.F. and Tate, M.E. The structure of myo-inositol pentaphosphates. Ann. N.Y. Acad. Sci. 165 (1969) 526-532. [PMID: 4310376]
3. Irving, G.C.J. and Cosgrove, D.J. Inositol phosphate phosphatases of microbiological origin: the inositol pentaphosphate products of Aspergillus ficuum phytases. J. Bacteriol. 112 (1972) 434-438. [PMID: 4342816]
4. Cosgrove, D.J. Inositol phosphates: their chemistry, biochemistry, and physiology., Elsevier, Amsterdam, 1980
Common name: 4-phytase
Reaction: myo-inositol hexakisphosphate + H2O = 1D-myo-inositol 1,2,3,4,5-pentakisphosphate + phosphate
Other name(s): 6-phytase (name based on 1L-numbering system and not 1D-numbering); phytase; phytate 6-phosphatase
Systematic name: myo-inositol-hexakisphosphate 6-phosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9001-89-2
References:
1. Johnson, L.F. and Tate, M.E. The structure of myo-inositol pentaphosphates. Ann. N.Y. Acad. Sci. 165 (1969) 526-532. [PMID: 4310376]
2. Tomlinson, R.V. and Ballou, C.E. Myoinositol polyphosphate intermediates in the dephosphorylation of phytic acid by phytase. Biochemistry 1 (1962) 166-171.
3. Lim, P.E. and Tate, M.E. The phytases. II. Properties of phytase fractions F1 and F2 from wheat bran and the myo-inositol phosphates produced by fraction F2. Biochim. Biophys. Acta 302 (1973) 316-328. [PMID: 4349266]
4. Cosgrove, D.J. Inositol phosphates: their chemistry, biochemistry, and physiology., Elsevier, Amsterdam, 1980
Common name: 5-phytase
Reaction: myo-inositol hexakisphosphate + H2O = 1L-myo-inositol 1,2,3,4,6-pentakisphosphate + phosphate
Systematic name: myo-inositol-hexakisphosphate 5-phosphohydrolase
Comments: The enzyme attacks the product of the above reaction more slowly to yield Ins(1,2,3)P3.
References:
1. Barrientos, L., Scott, J.J. and Murthy, P.P. Specificity of hydrolysis of phytic acid by alkaline phytase from lily pollen. Plant Physiol. 106 (1994) 1489-1495. [PMID: 7846160]
[EC 3.1.4.47 Transferred entry: now EC 4.6.1.14, glycosylphosphatidylinositol diacylglycerol-lyase (EC 3.1.4.47 created 1989, deleted 2002)]
Common name: glycosylphosphatidylinositol phospholipase D
Reaction: 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol + H2O = 6-(α-D-glucosaminyl)-1D-myo-inositol + phosphatidate
For diagram click here.
Other name(s): GPI-PLD; glycoprotein phospholipase D; phosphatidylinositol phospholipase D; phosphatidylinositol-specific phospholipase D
Systematic name: glycoprotein-phosphatidylinositol phosphatidohydrolase
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 glycosylphosphatidylinositol (GPI) anchors, but does so by hydrolysis, whereas glycosylphosphatidylinositol diacylglycerol-lyase (EC 4.6.1.14) does so by elimination. It acts on plasma membranes only after solubilization of the substrate with detergents or solvents, but it may act on intracellular membranes.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 113756-14-2
References:
1. Low, M.G. and Prasad, A.R.S. A phospholipase D specific for the phosphatidylinositol anchor of cell-surface proteins is abundant in plasma. Proc. Natl. Acad. Sci. USA 85 (1988) 980-984. [PMID: 3422494]
2. Malik, A.-S. and Low, M.G. Conversion of human placental alkaline phosphatase from a high Mr form to a low Mr form during butanol extraction. An investigation of the role of endogenous phosphoinositide-specific phospholipases. Biochem. J. 240 (1986) 519-527. [PMID: 3028377]
3. Li, J.Y., Hollfelder, K., Huang, K.S. and Low, M.G. Structural features of GPI-specific phospholipase D revealed by fragmentation and Ca2+ binding studies. J. Biol. Chem. 269 (1994) 28963-28971. [PMID: 7961859]
4. Deeg, M.A,, Vierman, E.L. and Cheung, M.C. GPI-specific phospholipase D associates with an apoA-I- and apoA-IV-containing complex. J. Lipid Res. 42 (2001) 442-451. [PMID: 11254757]
Common name: RNase Z
Reaction: endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule
Other name(s): 3 tRNase; tRNA 3 endonuclease
Comments: No cofactor requirements. An homologous enzyme to that found in Arabidopsis thaliana has been found in Methanococcus janaschii.
References:
1. Schiffer, S., Rösch, S. and Marchfelder, A. Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. EMBO J. 21 (2002) 2769-2777. [PMID: 12032089]
2. Mayer, M., Schiffer, S. and Marchfelder, A. tRNA 3' processing in plants: nuclear and mitochondrial activities differ. Biochemistry 39 (2000) 2096-2105. [PMID: 10684660]
3. Schiffer, S., Helm, M., Theobald-Dietrich, A., Giege, R. and Marchfelder, A. The plant tRNA 3' processing enzyme has a broad substrate spectrum. Biochemistry 40 (2001) 8264-8272. [PMID: 11444972]
4. Kunzmann, A., Brennicke, A. and Marchfelder, A. 5' end maturation and RNA editing have to precede tRNA 3' processing in plant mitochondria. Proc. Natl. Acad. Sci. USA 95 (1998) 108-113. [PMID: 9419337]
5. Mörl, M. and Marchfelder, A. The final cut. The importance of tRNA 3'-processing. EMBO Rep. 2 (2001) 17-20. [PMID: 11252717]
Common name: N-acetylglucosaminylphosphatidylinositol deacetylase
Reaction: 6-(N-acetyl-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol + H2O = 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol + acetate
For diagram click here.
Other name(s): N-acetyl-D-glucosaminylphosphatidylinositol acetylhydrolase; N-acetylglucosaminylphosphatidylinositol de-N-acetylase; GlcNAc-PI de-N-acetylase; GlcNAc-PI deacetylase; acetylglucosaminylphosphatidylinositol deacetylase
Systematic name: 6-(N-acetyl-α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol acetylhydrolase
Comments: Involved in the second step of glycosylphosphatidylinositol (GPI) anchor formation in all eukaryotes. The enzyme appears to be composed of a single subunit (PIG-L in mammalian cells and GPI12 in yeast). In some species, the long-chain sn-1-acyl group of the phosphatidyl group is replaced by a long-chain alkyl or alk-1-enyl group.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number:
References:
1. Doering, T.L., Masteron, W.J., Englund, P.T. and Hart, G.W. Biosynthesis of the glycosyl phosphatidylinositol membrane anchor of the trypanosome variant surface glycoprotein. Origin of the non-acetylated glucosamine. J. Biol. Chem. 264 (1989) 11168-11173. [PMID: 2525555]
2. Nakamura, N., Inoue, N., Watanabe, R., Takahashi, M., Takeda, J., Stevens, V.L. and Kinoshita, T. Expression cloning of PIG-L, a candidate N-acetylglucosaminyl-phosphatidylinositol deacetylase. J. Biol. Chem. 272 (1997) 15834-15840. [PMID: 9188481]
3. Watanabe, R., Ohishi, K., Maeda, Y., Nakamura, N. and Kinoshita, T. Mammalian PIG-L and its yeast homologue Gpi12p are N-acetylglucosaminylphosphatidylinositol de-N-acetylases essential in glycosylphosphatidylinositol biosynthesis. Biochem. J. 339 (1999) 185-192. [PMID: 10085243]
4. Smith, T.K, Crossman, A., Borissow, C.N., Paterson, M.J., Dix, A., Brimacombe, J.S. and Ferguson, M.A.J. Specificity of GlcNAc-PI de-N-acetylase of GPI biosynthesis and synthesis of parasite-specific suicide substrate inhibitors. EMBO J. 20 (2001) 3322-3332. [PMID: 11432820]
Common name: undecaprenyl-diphosphatase
Reaction: undecaprenyl diphosphate + H2O = undecaprenyl phosphate + phosphate
For diagram click here.
Other name(s): C55-isoprenyl diphosphatase; C55-isoprenyl pyrophosphatase; isoprenyl pyrophosphatase
Systematic name: undecaprenyl-diphosphate phosphohydrolase
Comments: The undecaprenol involved is ditrans,octacis-undecaprenol (for definitions, click here).
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9077-80-9
References:
1. Goldman, R. and Strominger, J.L. Purification and properties of C55-isoprenylpyrophosphate phosphatase from Micrococcus lysodeikticus. J. Biol. Chem. 247 (1972) 5116-5122. [PMID: 4341539]
Common name: 4-hydroxyphenylpyruvate decarboxylase
Reaction: 4-hydroxyphenylpyruvate = 4-hydroxyphenylacetaldehyde + CO2
For diagram click here.
Systematic name: 4-hydroxyphenylpyruvate carboxy-lyase
Comments: Reacts with dopamine to give the benzylisoquinoline alkaloid skeleton.
References:
1. Rueffer, M. and Zenk, M.H. Distant precursors of benzylisoquinoline alkaloids and their enzymatic formation. Z. Naturforsch. C: Biosci. 42 (1987) 319-332.
[EC 4.1.2.15 Transferred entry: now EC 2.5.1.54, 3-deoxy-7-phosphoheptulonate synthase (EC 4.1.2.15 created 1965, modified 1976, deleted 2002)]
[EC 4.1.2.16 Transferred entry: now EC 2.5.1.55, 3-deoxy-8-phosphooctulonate synthase (EC 4.1.2.16 created 1965, deleted 2002)]
[EC 4.1.3.2 Transferred entry: now EC 2.3.3.9, malate synthase (EC 4.1.3.2 created 1961, deleted 2002)]
[EC 4.1.3.5 Transferred entry: now EC 2.3.3.10, hydroxymethylglutaryl-CoA synthase (EC 4.1.3.5 created 1961, deleted 2002)]
[EC 4.1.3.7 Transferred entry: now EC 2.3.3.1, citrate (Si)-synthase (EC 4.1.3.7 created 1961, deleted 2002)]
[EC 4.1.3.8 Transferred entry: now EC 2.3.3.8, ATP citrate synthase (EC 4.1.3.8 created 1965, modified 1986, deleted 2002)]
[EC 4.1.3.9 Transferred entry: now EC 2.3.3.11, 2-hydroxyglutarate synthase (EC 4.1.3.9 created 1965, deleted 2002)]
[EC 4.1.3.10 Transferred entry: now EC 2.3.3.7, 3-ethylmalate synthase (EC 4.1.3.10 created 1965, modified 1983, deleted 2002)]
[EC 4.1.3.11 Transferred entry: now EC 2.3.3.12, 3-propylmalate synthase (EC 4.1.3.11 created 1972, deleted 2002)]
[EC 4.1.3.12 Transferred entry: now EC 2.3.3.13, 2-isopropylmalate synthase (EC 4.1.3.12 created 1972, deleted 2002)]
[EC 4.1.3.15 Transferred entry: now EC 2.2.1.5, 2-hydroxy-3-oxoadipate synthase (EC 4.1.3.15 created 1972, deleted 2002)]
[EC 4.1.3.18 Transferred entry: now EC 2.2.1.6, acetolactate synthase (EC 4.1.3.18 created 1972, deleted 2002)]
[EC 4.1.3.19 Transferred entry: now EC 2.5.1.56, N-acetylneuraminate synthase (EC 4.1.2.19 created 1972, deleted 2002)]
[EC 4.1.3.20 Transferred entry: now EC 2.5.1.57, N-acylneuraminate-9-phosphate synthase (EC 4.1.3.20 created 1972, deleted 2002)]
[EC 4.1.3.21 Transferred entry: now EC 2.3.3.14, homocitrate synthase (EC 4.1.3.21 created 1972, deleted 2002)]
[EC 4.1.3.23 Transferred entry: now EC 2.3.3.2, decylcitrate synthase (EC 4.1.3.23 created 1972, deleted 2002)]
[EC 4.1.3.28 Transferred entry: now EC 2.3.3.3, citrate (Re)-synthase (EC 4.1.3.28 created 1972, deleted 2002)]
[EC 4.1.3.29 Transferred entry: now EC 2.3.3.4, decylhomocitrate synthase (EC 4.1.3.29 created 1976, deleted 2002)]
[EC 4.1.3.31 Transferred entry: now EC 2.3.3.5, 2-methylcitrate synthase (EC 4.1.3.31 created 1978, deleted 2002)]
[EC 4.1.3.33 Transferred entry: now EC 2.3.3.6, 2-ethylmalate synthase (EC 4.1.3.33 created 1983, deleted 2002)]
[EC 4.1.3.37 Transferred entry: now EC 2.2.1.7, 1-deoxy-D-xylulose 5-phosphate synthase (EC 4.1.3.37 created 2001, deleted 2002)]
Common name: tryptophan synthase
Reaction: L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate
For diagram click here and mechanism here.
Other name(s): L-tryptophan synthetase; indoleglycerol phosphate aldolase; tryptophan desmolase; tryptophan synthetase
Systematic name: L-serine hydro-lyase (adding indoleglycerol-phosphate)
Comments: A pyridoxal-phosphate protein. The α-subunit catalyses the conversion of 1-(indol-3-yl)glycerol 3-phosphate to indole and glyceraldehyde 3-phosphate. The indole then migrates to the β-subunit where, with serine in the presence of pyridoxal 5'-phosphate, it is converted to tryptophan. Also catalyses the conversion of serine and indole into tryptophan and water, and of indoleglycerol phosphate into indole and glyceraldehyde phosphate (the latter reaction was listed formerly as EC 4.1.2.8). In some organisms, this enzyme is part of a multifunctional protein, together with one or more other components of the system for the biosynthesis of tryptophan [EC 2.4.2.18 (anthranilate phosphoribosyltransferase ), EC 4.1.1.48 (indole-3-glycerol-phosphate synthase), EC 4.1.3.27 (anthranilate synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase)].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, WIT, CAS registry number: 9014-52-2
References:
1. Crawford, I.P. and Yanofsky, C. On the separation of the tryptophan synthetase of Eschericia coli into two protein components. Proc. Natl. Acad. Sci. USA 44 (1958) 1161-1170.
2. Creighton, T.E. and Yanofsky, C. Chorismate to tryptophan (Escherichia coli) - anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase. Methods Enzymol. 17A (1970) 365-380.
3. Hütter, R., Niederberger, P. and DeMoss, J.A. Tryptophan biosynthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55-77.
4. Hyde, C.C., Ahmed, S.A., Padlan, E.A., Miles, E.W. and Davies, D.R. Three-dimensional structure of the tryptophan synthase α2β2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263 (1988) 17857-17871. [PMID: 3053720]
5. Woehl, E. and Dunn, M.F. Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase α-, β-, and αβ-reactions. Biochemistry 38 (1999) 7131-7141. [PMID: 10353823]
Common name: chorismate synthase
Reaction: 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate
For diagram click here and mechanism here.
Systematic name: 5-O-(1-carboxyvinyl)-3-phosphoshikimate phosphate-lyase
Comments: Requires FMN. The reaction goes via a radical mechanism that involves reduced FMN and its semiquinone (FMNH•). Shikimate is numbered so that the double-bond is between C-1 and C-2, but some earlier papers numbered the ring in the reverse direction.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9077-07-0
References:
1. Gaertner, F.H. and Cole, K.W. Properties of chorismate synthase in Neurospora crassa. J. Biol. Chem. 248 (1973) 4602-4609. [PMID: 4146266]
2. Morell, H., Clark, M.J., Knowles, P.F. and Sprinson, D.B. The enzymic synthesis of chorismic and prephenic acids from 3-enolpyruvylshikimic acid 5-phosphate. J. Biol. Chem. 242 (1967) 82-90. [PMID: 4289188]
3. Welch, G.R., Cole, K.W. and Gaertner, F.H. Chorismate synthase of Neurospora crassa: a flavoprotein. Arch. Biochem. Biophys. 165 (1974) 505-518. [PMID: 4155270]
4. Bornemann, S., Lowe, D.J. and Thorneley, R.N. The transient kinetics of Escherichia coli chorismate synthase: substrate consumption, product formation, phosphate dissociation, and characterization of a flavin intermediate. Biochemistry 35 (1996) 9907-9916. [PMID: 8703965]
5. Bornemann, S., Theoclitou, M.E., Brune, M., Webb, M.R., Thorneley, R.N. and Abell, C. A secondary β deuterium kinetic isotope effect in the chorismate synthase reaction. Bioorg. Chem. 28 (2000) 191-204. [PMID: 11034781]
6. Osborne, A., Thorneley, R.N., Abell, C. and Bornemann, S. Studies with substrate and cofactor analogues provide evidence for a radical mechanism in the chorismate synthase reaction. J. Biol. Chem. 275 (2000) 35825-35830. [PMID: 10956653]
Common name: taxadiene synthase
Reaction: geranylgeranyl diphosphate = taxa-4,11-diene + diphosphate
For reaction pathway click here.
Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cyclizing, taxadiene forming)
Comments: The cyclization involves a 1,5-hydride shift.
References:
1. Koepp, A.E., Hezari, M., Zajicek, J., Vogel, B.S., LaFever, R.E., Lewis, N.G. and Croteau, R. Cyclization of geranylgeranyl diphosphate to taxa-4(5),11(12)-diene is the committed step of taxol biosynthesis in Pacific yew. J. Biol. Chem. 270 (1995) 8686-8690. [PMID: 7721772]
2. Hezari, M., Lewis, N.G. and Croteau, R. Purification and characterization of taxa-4(5),11(12)-diene synthase from Pacific yew (Taxus brevifolia) that catalyzes the first committed step of taxol biosynthesis. Arch. Biochem. Biophys. 322 (1995) 437-444. [PMID: 7574719]
3. Lin, X., Hezari, M., Koepp, A.E., Floss, H.G. and Croteau, R. Mechanism of taxadiene synthase, a diterpene cyclase that catalyzes the first step of taxol biosynthesis in Pacific yew. Biochemistry 35 (1996) 2968-2977. [PMID: 8608134]
4. Hezari, M., Ketchum, R.E., Gibson, D.M. and Croteau, R. Taxol production and taxadiene synthase activity in Taxus canadensis cell suspension cultures. Arch. Biochem. Biophys. 337 (1997) 185-90. [PMID: 9016812]
5. Williams, D.C., Carroll, B.J., Jin, Q., Rithner, C.D., Lenger, S.R., Floss, H.G., Coates, R.M., Williams, R.M. and Croteau, R. Intramolecular proton transfer in the cyclization of geranylgeranyl diphosphate to the taxadiene precursor of taxol catalyzed by recombinant taxadiene synthase. Chem. Biol. 7 (2000) 969-977.
Common name: abietadiene synthase
Reaction: (+)-copalyl diphosphate = (-)-abietadiene + diphosphate
For reaction pathway click here.
Systematic name: copalyl-diphosphate diphosphate-lyase (cyclizing)
Comments: Part of a bifunctional enzyme involved in the biosynthesis of abietadiene. See also EC 5.5.1.12 (copalyl diphosphate synthase). Requires Mg2+
References:
1. Peters, R.J., Flory, J.E., Jetter, R., Ravn, M.M., Lee, H.J., Coates, R.M. and Croteau, R.B. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry 39 (2000) 15592-15602. [PMID: 11112547]
2. Peters, R.J., Ravn, M.M., Coates, R.M. and Croteau, R.B. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J. Am. Chem. Soc. 123 (2001) 8974-8978. [PMID: 11552804]
3. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc. Natl. Acad. Sci. USA 99 (2002) 580-584. [PMID: 11805316]
4. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry 41 (2002) 1836-1842. [PMID: 11827528 ]
5. Ravn, M.M., Peters, R.J., Coates, R.M. and Croteau, R. Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. J. Am. Chem. Soc. 124 (2002) 6998-7006. [PMID: 12059223]
Common name: ent-kaurene synthase
Reaction: ent-copalyl diphosphate = ent-kaurene + diphosphate
For reaction pathway click here.
Other name(s): ent-kaurene synthase B; ent-kaurene synthetase B
Systematic name: ent-copalyl-diphosphate diphosphate-lyase (cyclizing)
Comments: Part of a bifunctional enzyme involved in the biosynthesis of ent-kaurene. See also EC 5.5.1.13 (ent-copalyl diphosphate synthase)
References:
1. Fall, R.R., West, C.A. Purification and properties of kaurene synthetase from Fusarium moniliforme. J. Biol. Chem. 246 (1971) 6913-6928. [PMID: 4331199]
2. Yamaguchi, S., Saito, T., Abe, H., Yamane, H., Murofushi, N. and Kamiya, Y. Molecular cloning and characterization of a cDNA encoding the gibberellin biosynthetic enzyme ent-kaurene synthase B from pumpkin (Cucurbita maxima L.). Plant J. 10 (1996) 203-213. [PMID: 8771778]
3. Kawaide, H., Imai, R., Sassa, T. and Kamiya, Y. Ent-kaurene synthase from the fungus Phaeosphaeria sp. L487. cDNA isolation, characterization, and bacterial expression of a bifunctional diterpene cyclase in fungal gibberellin biosynthesis. J. Biol. Chem. 272 (1997) 21706-21712. [PMID: 9268298]
4. Toyomasu, T., Kawaide, H., Ishizaki, A., Shinoda, S., Otsuka, M., Mitsuhashi, W. and Sassa, T. Cloning of a full-length cDNA encoding ent-kaurene synthase from Gibberella fujikuroi: functional analysis of a bifunctional diterpene cyclase. Biosci. Biotechnol. Biochem. 64 (2000) 660-664. [PMID: 10803977]
[EC 4.2.99.8 Transferred entry: now EC 2.5.1.47, cysteine synthase (EC 4.2.99.8 created 1972, modified 1976, modified 1990, deleted 2002)]
[EC 4.2.99.9 Transferred entry: now EC 2.5.1.48, cystathionine γ-synthase (EC 4.2.99.9 created 1972, deleted 2002)]
[EC 4.2.99.10 Transferred entry: now EC 2.5.1.49, O-acetylhomoserine aminocarboxypropyltransferase (EC 4.2.99.10 created 1972, deleted 2002)]
[EC 4.2.99.13 Transferred entry: now EC 2.5.1.50, zeatin 9-aminocarboxyethyltransferase (EC 4.2.99.13 created 1984, deleted 2002)]
[EC 4.2.99.14 Transferred entry: now EC 2.5.1.51, β-pyrazolylalanine synthase (EC 4.2.99.14 created 1989 (EC 4.2.99.17 incorporated 1992), deleted 2002)]
[EC 4.2.99.15 Transferred entry: now EC 2.5.1.52, L-mimosine synthase (EC 4.2.99.15 created 1989, deleted 2002)]
[EC 4.2.99.16 Transferred entry: now EC 2.5.1.53, uracilylalanine synthase (EC 4.2.99.16 created 1990, deleted 2002)]
[EC 4.4.1.18 Transferred entry: now EC 1.8.3.5, prenylcysteine lyase (EC 4.4.1.18 created 2000, deleted 2002)]
Common 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 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
Systematic name: 6-(α-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol diacylglycerol-lyase (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, WIT, 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. [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. [PMID: 10764777]
Common name: FAD-AMP lyase (cyclizing)
Reaction: FAD = AMP + riboflavin cyclic-4',5'-phosphate
Other name(s): FMN cyclase
Systematic name: FAD AMP-lyase (cyclic-FMN-forming)
Comments: Requires Mn2+ or Co2+. While FAD was the best substrate tested [2], the enzyme also splits ribonucleoside diphosphate-X compounds in which X is an acyclic or cyclic monosaccharide or derivative bearing an X-OH group that is able to attack internally the proximal phosphorus with the geometry necessary to form a P=X product; either a five-atom monocyclic phosphodiester or a cis-bicyclic phosphodiester-pyranose fusion. The reaction is strongly inhibited by ADP or ATP but is unaffected by the presence of the product, cFMN.
References:
1. Fraiz, F.J., Pinto, R.M., Costas, M.J., Avalos, M., Canales, J., Cabezas, A. and Cameselle, J.C. Enzymic formation of riboflavin 4',5'-cyclic phosphate from FAD: evidence for a specific low-Km FMN cyclase in rat liver. Biochem. J. 330 (1998) 881-888. [PMID: 9480905]
2. Cabezas, A., Pinto, R.M., Fraiz, F., Canales, J., Gonzalez-Santiago, S., and Cameselle, J.C. Purification, characterization, and substrate and inhibitor structure-activity studies of rat liver FAD-AMP lyase (cyclizing): preference for FAD and specificity for splitting ribonucleoside diphosphate-X into ribonucleotide and a five-atom cyclic phosphodiester of X, either a monocyclic compound or a cis-bicyclic phosphodiester-pyranose fusion. Biochemistry 40 (2001) 13710-13722. [PMID: 11695920]
Common name: isopenicillin-N epimerase
Reaction: isopenicillin N = penicillin N
For diagram 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).
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. [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. [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.
Common name: maltose epimerase
Reaction: α-maltose = β-maltose
Systematic name: maltose 1-epimerase
Comments: The enzyme catalyses the interconversion of α and β anomers of maltose more effectively than those of disaccharides such as lactose and cellobiose.
References:
1. Shirokane, Y. and Suzuki, M. A novel enzyme, maltose 1-epimerase from Lactobacillus brevis IFO 3345. FEBS Lett. 367 (1995) 177-179. [PMID: 7796915]
Common name: peptidylprolyl isomerase
Reaction: peptidylproline (ω=180) = peptidylproline (ω=0)
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, WIT, 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. [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. [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. [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. [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. [PMID: 11859194 ]
Common name: squalene—hopene cyclase
Reaction: (1) squalene = hop-22(29)-ene
(2) squalene + H2O = hopan-22-ol
For reaction pathway click here.
Systematic name: squalene mutase (cyclizing)
Comment: The enzyme produces a constant ratio of about 5:1 hopene:hopanol.
References:
1. Seckler, B. and Poralla, K. Characterization and partial purification of squalene-hopene cyclase from Bacillus acidocaldarius. Biochim. Biophys. Acta 881 (1986) 356-363.
2. Hoshino, T. and Sato, T. Squalene-hopene cyclase: catalytic mechanism and substrate recognition. Chem. Commun. (2002) 291-301.
Common name: copalyl diphosphate synthase
Reaction: geranylgeranyl diphosphate = (+)-copalyl diphosphate
For reaction pathway click here.
Systematic name: (+)-copalyl-diphosphate lyase (decyclizing)
Comments: Part of a bifunctional enzyme involved in the biosynthesis of abietadiene. See also EC 4.2.3.18 (abietadiene synthase)
References:
1. Peters, R.J., Flory, J.E., Jetter, R., Ravn, M.M., Lee, H.J., Coates, R.M. and Croteau, R.B. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry 39 (2000) 15592-15602. [PMID: 11112547]
2. Peters, R.J., Ravn, M.M., Coates, R.M. and Croteau, R.B. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J. Am. Chem. Soc. 123 (2001) 8974-8978. [PMID: 11552804]
3. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc. Natl. Acad. Sci. USA 99 (2002) 580-584. [PMID: 11805316]
4. Ravn, M.M., Peters, R.J., Coates, R.M. and Croteau, R. Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. J. Am. Chem. Soc. 124 (2002) 6998-7006. [PMID: 12059223]
5. Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry 41 (2002) 1836-1842. [PMID: 11827528 ]
Common name: ent-copalyl diphosphate synthase
Reaction: geranylgeranyl diphosphate = ent-copalyl diphosphate
For reaction pathway click here.
Other name(s): ent-kaurene synthase A; ent-kaurene synthetase A
Systematic name: ent-copalyl-diphosphate lyase (decyclizing)
Comments: Part of a bifunctional enzyme involved in the biosynthesis of kaurene. See also EC 4.2.3.19 (ent-kaurene synthase)
References:
1. Fall, R.R., West, C.A. Purification and properties of kaurene synthetase from Fusarium moniliforme. J. Biol. Chem. 246 (1971) 6913-6928. [PMID: 4331199]
2. Sun, T.P. and Kamiya, Y. The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin biosynthesis. Plant Cell 6 (1994) 1509-1518. [PMID: 7994182]
3. Kawaide, H., Imai, R., Sassa, T. and Kamiya, Y. Ent-kaurene synthase from the fungus Phaeosphaeria sp. L487. cDNA isolation, characterization, and bacterial expression of a bifunctional diterpene cyclase in fungal gibberellin biosynthesis. J. Biol. Chem. 272 (1997) 21706-21712. [PMID: 9268298]
4. Toyomasu, T., Kawaide, H., Ishizaki, A., Shinoda, S., Otsuka, M., Mitsuhashi, W. and Sassa, T. Cloning of a full-length cDNA encoding ent-kaurene synthase from Gibberella fujikuroi: functional analysis of a bifunctional diterpene cyclase. Biosci. Biotechnol. Biochem. 64 (2000) 660-664. [PMID: 10803977]
Common name: tyrosine—tRNA ligase
Reaction: ATP + L-tyrosine + tRNATyr = AMP + diphosphate + L-tyrosyl-tRNATyr
Other name(s): tyrosyl-tRNA synthetase; L-tyrosine-tRNATyr ligase (AMP-forming); tyrosyl-transfer ribonucleate synthetase; tyrosyl-transfer RNA synthetase; tyrosyl-transfer ribonucleic acid synthetase; tyrosyl-tRNA ligase; tyrosine-transfer RNA ligase; tyrosine-transfer ribonucleate synthetase; tyrosine translase; tyrosine tRNA synthetase
Systematic name: L-tyrosine:tRNATyr ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9023-45-4
References:
1. Allen, E.H., Glassman, E. and Schweet, R.S. Incorporation of amino acids into ribonucleic acid. I. The role of activating enzymes. J. Biol. Chem. 235 (1960) 1061-1067.
2. Cowles, J.R. and Key, J.L. Demonstration of two tyrosyl-tRNA synthetases of pea roots. Biochim. Biophys. Acta 281 (1972) 33-44. [PMID: 4563531]
3. Holley, R.W., Brunngraber, E.F., Saad, F. and Williams, H.H. Partial purification of the threonine- and tyrosine-activating enzymes from rat liver, and the effect of potassium ions on the activity of the tyrosine enzyme. J. Biol. Chem. 236 (1961) 197-199.
4. Schweet, R.S. and Allen, E.H. Purification and properties of tyrosine-activating enzyme of hog pancreas. J. Biol. Chem. 233 (1958) 1104-1108.
5. Brick, P., Bhat, T.N. and Blow, D.M. Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J. Mol. Biol. 208 (1989) 83-98. [PMID: 2504923]
Common name: tryptophan—tRNA ligase
Reaction: ATP + L-tryptophan + tRNATrp = AMP + diphosphate + L-tryptophan-tRNATrp
Other name(s): tryptophanyl-tRNA synthetase; L-tryptophan-tRNATrp ligase (AMP-forming); tryptophanyl-transfer ribonucleate synthetase; tryptophanyl-transfer ribonucleic acid synthetase; tryptophanyl-transfer RNA synthetase; tryptophanyl ribonucleic synthetase; tryptophanyl-transfer ribonucleic synthetase; tryptophanyl-tRNA synthase; tryptophan translase; TrpRS
Systematic name: L-tryptophan:tRNATrp ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9023-44-3
References:
1. Davie, E.W., Koningsberger, V.V. and Lipmann, F. The isolation of a tryptophan-activating enzyme from pancreas. Arch. Biochem. Biophys. 65 (1956) 21-28.
2. Preddie, E.C. Tryptophanyl transfer ribonucleic acid synthetase from bovine pancreas. II. The chemically different subunits. J. Biol. Chem. 244 (1969) 3958-3968. [PMID: 5805407]
3. Wong, K.K., Meister, A. and Moldave, K. Enzymic formation of ribonucleic acid-amino acid from synthetic aminoacyladenylate and ribonucleic acid. Biochim. Biophys. Acta 36 (1959) 531-533.
Common name: methionine—tRNA ligase
Reaction: ATP + L-methionine + tRNAMet = AMP + diphosphate + L-methionyl-tRNAMet
Other name(s): methionyl-tRNA synthetase; methionyl-transfer ribonucleic acid synthetase; methionyl-transfer ribonucleate synthetase; methionyl-transfer RNA synthetase; methionine translase; MetRS
Systematic name: L-methionine:tRNAMet ligase (AMP-forming)
Comments: In those organisms producing N-formylmethionyl-tRNAfMet for translation initiation, this enzyme also recognizes the initiator tRNAfMet and catalyses the formation of L-methionyl-tRNAfMet, the substrate for EC 2.1.2.9, methionyl-tRNA formyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, WIT, CAS registry number: 9033-22-1
References:
1. Bergmann, F.H., Berg, P. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. II. The preparation of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid synthetases from Escherichia coli. J. Biol. Chem. 236 (1961) 1735-1740.
2. Lee, C.P., Dyson, M.R., Mandal, N., Varshney, U., Bahramian, B. and RajBhandary, U.L. Striking effects of coupling mutations in the acceptor stem on recognition of tRNAs by Escherichia coli Met-tRNA synthetase and Met-tRNA transformylase.
Common name: serine—tRNA ligase
Reaction: ATP + L-serine + tRNASer = AMP + diphosphate + L-seryl-tRNASer
Other name(s): seryl-tRNA synthetase; SerRS; seryl-transfer ribonucleate synthetase; seryl-transfer RNA synthetase; seryl-transfer ribonucleic acid synthetase; serine translase
Systematic name: L-serine:tRNASer ligase (AMP-forming)
Comments: This enzyme also recognizes tRNASec, the special tRNA for selenocysteine, and catalyses the formation of L-seryl-tRNASec, the substrate for EC 2.9.1.1, L-seryl-tRNASec selenium transferase.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
WIT,
CAS registry number: 9023-48-7
References:
1. Katze, J.R. and Konigsberg, W. Purification and properties of seryl transfer ribonucleic acid synthetase from Escherichia coli. J. Biol. Chem. 245 (1970) 923-930. [PMID: 70130512]
2. Makman, M.H. and Cantoni, G.L. Isolation of seryl and phenylalanyl ribonucleic acid synthetases from baker's yeast. Biochemistry 4 (1965) 1434-1442.
3. Webster, L.T. and Davie, E.W. Purification and properties of serine-activating enzyme from beef pancreas. J. Biol. Chem. 236 (1961) 479-484.
4. Ohama, T., Yang, D.C. and Hatfield, D.L. Selenocysteine tRNA and serine
tRNA are aminoacylated by the same synthetase, but may manifest different
identities with respect to the long extra arm. Arch. Biochem. Biophys. 315 (1994) 293-301. [PMID: 7986071]
Common name: aspartate—tRNAAsn ligase
Reaction: ATP + L-aspartate + tRNAAsx = AMP + diphosphate + Asp-tRNAAsx
Other name(s): nondiscriminating aspartyl-tRNA synthetase
Systematic name: L-aspartate:tRNAAsx ligase (AMP-forming)
Comments: When this enzyme acts on tRNAAsp, it catalyses the same reaction as EC 6.1.1.12, aspartate—tRNA ligase. It has, however, diminished discrimination, so that it can also form Asp-tRNAAsn. This relaxation of specificity has been found to result from the absence of a loop in the tRNA that specifically recognizes the third position of the anticodon [1]. This accounts for the ability of this enzyme in, for example, Thermus thermophilus, to recognize both tRNAAsp (GUC anticodon) and tRNAAsn (GUU anticodon). The Asp-tRNAAsn is not used in protein synthesis until it is converted by EC 6.3.5.6, asparaginyl-tRNA synthase (glutamine-hydrolysing), into Asn-tRNAAsn.
References:
1. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]
2. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J.C. and Moras, D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 17 (1998) 5227-5237. [PMID: 9724658]
3. Becker, H.D. and Kern, D. Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl. Acad. Sci. USA 95 (1998) 12832-12837. [PMID: 9789000]
Common name: glutamate—tRNAGln ligase
Reaction: ATP + L-glutamate + tRNAGlx = AMP + diphosphate + Glu-tRNAGlx
Other name(s): nondiscriminating glutamyl-tRNA synthetase
Systematic name: L-glutamate:tRNAGlx ligase (AMP-forming)
Comments: When this enzyme acts on tRNAGlu, it catalyses the same reaction as EC 6.1.1.17, glutamate—tRNA ligase. It has, however, diminished discrimination, so that it can also form Glu-tRNAGln. This relaxation of specificity has been found to result from the absence of a loop in the tRNA that specifically recognizes the third position of the anticodon [1]. This accounts for the ability of this enzyme in, for example, Bacillus subtilis, to recognize both tRNA1Gln (UUG anticodon) and tRNAGlu (UUC anticodon) but not tRNA2Gln (CUG anticodon). The ability of this enzyme to recognize both tRNAGlu and one of the tRNAGln isoacceptors derives from their sharing a major identity element, a hypermodified derivative of U34 (5-methylaminomethyl-2-thiouridine). The Glu-tRNAGln is not used in protein synthesis until it is converted by EC 6.3.5.7, glutaminyl-tRNA synthase (glutamine-hydrolysing), into Gln-tRNAGln.
References:
1. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]
2. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J.C. and Moras, D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 17 (1998) 5227-5237. [PMID:9724658]
3. Kim, S.I. and Söll, D. Major identity element of glutamine tRNAs from Bacillus subtilis and Escherichia coli in the reaction with B. subtilis glutamyl-tRNA synthetase. Mol. Cells 8 (1998) 459-465. [PMID: 9749534]
Common name: lysine—tRNAPyl ligase
Reaction: ATP + L-lysine + tRNAPyl = AMP + diphosphate + L-lysyl-tRNAPyl
Glossary: pyrrolysine
Systematic name: L-lysine:tRNAPyl ligase (AMP-forming)
Comments: In organisms such as Methanosarcina barkeri that incorporate the modified amino acid pyrrolysine (Pyl) into certain methylamine methyltransferases, an unusual tRNAPyl, with a CUA anticodon, is charged with lysine by this class II aminoacyl—tRNA ligase. Pyrrolysine is N6-[(2R,3R)-3-R-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine, where R = Me, OH, or NH2. The tRNA and the ligase are encoded within the same gene cluster, and the ligase does not appear to be closely related to EC 6.1.1.6, lysine—tRNA ligase.
References:
1. Srinivasan, G., James, C.M. and Krzycki, J.A. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296 (2002) 1459-1462. [PMID: 12029131]
2. Hao, B., Gong, W., Ferguson, T.K., James, C.M., Krzycki, J.A. and Chan, M.K. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 1459 (2002) 1462-1466. [PMID: 12029132]
Common name: D-alanine—D-alanine ligase
Reaction: ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
For diagram click here.
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-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase), EC 6.3.2.8 (UDP-N-acetylmuramate—L-alanine ligase), EC 6.3.2.9 (UDP-N-acetylmuramoylalanine—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,
WIT,
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 only.
3. van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503-519. [PMID: 11699883]
Common name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase
Reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + L-lysine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine
For diagram click here.
Other name(s): MurE synthetase; UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine synthetase; uridine diphospho-N-acetylmuramoylalanyl-D-glutamyllysine synthetase; UPD-MurNAc-L-Ala-D-Glu:L-Lys ligase
Systematic name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:L-lysine γ-ligase (ADP-forming)
Comments: Involved with EC 6.3.2.4 (D-alanine—D-alanine ligase), EC 6.3.2.8 (UDP-N-acetylmuramate—L-alanine ligase), EC 6.3.2.9 (UDP-N-acetylmuramoylalanine—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). This enzyme adds lysine in some Gram-positive organisms; in others and in Gram-negative organisms EC 6.3.2.13 (UDP-N-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase) adds 2,6-diaminopimelate instead.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
WIT,
CAS registry number: 9023-51-2
References:
1. Ito, E. and Strominger, J.L. Enzymatic synthesis of the peptide in bacterial uridine nucleotides. I. Enzymatic addition of L-alanine, D-glutamic acid, and L-lysine. J. Biol. Chem. 237 (1962) 2689-2695.
2. van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503-519. [PMID: 11699883]
Common name: UDP-N-acetylmuramate—L-alanine ligase
Reaction: ATP + UDP-N-acetylmuramate + L-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanine
For diagram click here.
Other name(s): MurC synthetase; UDP-N-acetylmuramoyl-L-alanine synthetase; uridine diphospho-N-acetylmuramoylalanine synthetase; UDP-N-acetylmuramoylalanine synthetase; L-alanine-adding enzyme; UDP-acetylmuramyl-L-alanine synthetase; UDPMurNAc-L-alanine synthetase; L-Ala ligase; uridine diphosphate N-acetylmuramate:L-alanine ligase; uridine 5'-diphosphate-N-acetylmuramyl-L-alanine synthetase; uridine-diphosphate-N-acetylmuramate:L-alanine ligase; UDP-MurNAc:L-alanine ligase; alanine-adding enzyme; UDP-N-acetylmuramyl:L-alanine ligase
Systematic name: UDP-N-acetylmuramate:L-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-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase), EC 6.3.2.9 (UDP-N-acetylmuramoylalanine—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,
WIT,
CAS registry number: 9023-52-3
References:
1. Ito, E. and Strominger, J.L. Enzymatic synthesis of the peptide in bacterial uridine nucleotides. I. Enzymatic addition of L-alanine, D-glutamic acid, and L-lysine. J. Biol. Chem. 237 (1962) 2689-2695.
2. Nathenson, S.G., Strominger, J.L. and Ito, E. Enzymatic synthesis of the peptide in bacterial uridine nucleotides. IV. Purification and properties of D-glutamic acid-adding enzyme. J. Biol. Chem. 239 (1964) 1773-1776.
3. van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503-519. [PMID: 11699883]
Common name: UDP-N-acetylmuramoylalanine—D-glutamate ligase
Reaction: ATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
For diagram click here.
Other name(s): MurD synthetase; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; uridine diphospho-N-acetylmuramoylalanyl-D-glutamate synthetase; D-glutamate-adding enzyme; D-glutamate ligase; UDP-Mur-NAC-L-Ala:D-Glu ligase
Systematic name: UDP-N-acetylmuramoyl-L-alanine:glutamate 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—Llysine ligase) or EC 6.3.2.13 (UDP-N-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase), EC 6.3.2.8 (UDP-N-acetylmuramate—Lalanine 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,
WIT,
CAS registry number: 9023-59-0
References:
1. Ito, E. and Strominger, J.L. Enzymatic synthesis of the peptide in bacterial uridine nucleotides. I. Enzymatic addition of L-alanine, D-glutamic acid, and L-lysine. J. Biol. Chem. 237 (1962) 2689-2695.
2. van Heijenoort, J. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18 (2001) 503-519. [PMID: 11699883]
Common 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
For diagram click here.
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-acetylmuramoylalanyl-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-acetylmuramoylalanine—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-AlaÜD-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,
WIT,
CAS registry number: 9023-60-3
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]
Common name: UDP-N-acetylmuramoylalanyl-D-glutamate—2,6-diaminopimelate ligase
Reaction: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diamino-heptanedioate
For diagram click here.
Other name(s): MurE synthetase [ambiguous]; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-2,6-diamino-heptanedioate ligase (ADP-forming); UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase
Systematic name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:(L)-meso-2,6-diaminoheptanedioate γ-ligase (ADP-forming)
Comments: Involved with EC 6.3.2.4 (D-alanine—D-alanine ligase), EC 6.3.2.8 (UDP-N-acetylmuramate—L-alanine ligase), EC 6.3.2.9 (UDP-N-acetylmuramoylalanine—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). This enzyme adds diaminopimelate in Gram-negative organisms and in some Gram-positive organisms; in others EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase) adds lysine instead. It is the amino group of the L-centre of the diaminopimelate that is acylated.
Comments:
Links to other databases:
BRENDA,
EXPASY,
KEGG,
WIT,
CAS registry number: 9075-09-6
References:
1. Mizuno, Y. and Ito, E. Purification and properties of uridine diphosphate N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate ligase. J. Biol. Chem. 243 (1968) 2665-2672. [Medline UI: 4967958]
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 6.3.2.15 Deleted entry: UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase. The activity observed is due to EC 6.3.2.10, UDP-N-acetylmuramoyl-tripeptide—D-alanyl-D-alanine ligase. (EC 6.3.2.15 created 1976, deleted 2002)]
Common name: N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase
Reaction: L-2-aminohexanedioate + L-cysteine + L-valine + 3 ATP = N-[L-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + 3 AMP + 3 diphosphate
For diagram click here and possible mechanism click here.
Other name(s): L-δ-(α-aminoadipoyl)-L-cysteinyl-D-valine synthetase; ACV 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).
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. [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]
Common name: aerobactin synthase
Reaction: 4 ATP + citrate + N6-acetyl-N6-hydroxylysine = 4 ADP + 4 phosphate + aerobactin
Systematic name: citrate:N6-acetyl-N6-L-lysine ligase (ADP-forming)
Comments: Requires Mg2+.
References:
1. Appanna, D.L., Grundy, B.J., Szczepan, E.W. and Viswanatha, T. Aerobactin synthesis in a cell-free system of Aerobacter aerogenes 62-1 Biochim. Biophys. Acta 801 (1984) 437-443.
Common name: asparaginyl-tRNA synthase (glutamine-hydrolysing)
Reaction: ATP + Asp-tRNAAsn + L-glutamine = ADP + phosphate + Asn-tRNAAsn + L-glutamate
Other name(s): Asp-AdT; Asp-tRNAAsn amidotransferase; aspartyl-tRNAAsn amidotransferase
Systematic name: Asp-tRNAAsn:L-glutamine amido-ligase (ADP-forming)
Comments: This reaction forms part of a two-reaction system for producing asparaginyl-tRNA in Deinococcus radiodurans and other organisms lacking a specific enzyme for asparagine synthesis. In the first step, a non-discriminating ligase (EC 6.1.1.23, aspartate—tRNAAsn ligase) mischarges tRNAAsn with aspartate, leading to the formation of Asp-tRNAAsn. The Asp-tRNAAsn is not used in protein synthesis until the present enzyme converts it into Asn-tRNAAsn (Asp-tRNAAsp is not a substrate for this reaction). Ammonia or asparagine can substitute for the preferred substrate glutamine.
References:
1. Min, B., Pelaschier, J.T., Graham, D.E., Tumbula-Hansen, D. and Söll, D. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. USA 99 (2002) 2678-2683. [PMID: 11880622]
2. Curnow, A.W., Tumbula, D.L., Pelaschier, J.T., Min, B. and Söll, D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95 (1998) 12838-12843. [PMID: 9789001]
3. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]
Common name: glutaminyl-tRNA synthase (glutamine-hydrolysing)
Reaction: ATP + Glu-tRNAGln + L-glutamine = ADP + phosphate + Gln-tRNAGln + L-glutamate
Other name(s): Glu-AdT; Glu-tRNAGln amidotransferase; glutamyl-tRNAGln amidotransferase
Systematic name: Glu-tRNAGln:L-glutamine amido-ligase (ADP-forming)
Comments: In systems lacking discernible glutamine—tRNA ligase (EC 6.1.1.18), Gln-tRNAGln is formed by a two-enzyme system. In the first step, a nondiscriminating ligase (EC 6.1.1.24, glutamate—tRNAGln ligase) mischarges tRNAGln with glutamate, forming Glu-tRNAGln. The Glu-tRNAGln is not used in protein synthesis until the present enzyme converts it into Gln-tRNAGln (Glu-tRNAGlu is not a substrate for this reaction). Ammonia or asparagine can substitute for the preferred substrate glutamine.
References:
1. Horiuchi, K.Y., Harpel, M.R., Shen, L., Luo, Y., Rogers, K.C. and Copeland, R.A. Mechanistic studies of reaction coupling in Glu-tRNAGln amidotransferase. Biochemistry 40 (2001) 6450-6457. [PMID: 11371208]
2. Curnow, A.W., Tumbula, D.L., Pelaschier, J.T., Min, B. and Söll, D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95 (1998) 12838-12843. [PMID: 9789001]
3. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]
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