The Enzyme Database

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EC 2.7.11.11     
Accepted name: cAMP-dependent protein kinase
Reaction: ATP + a [protein]-(L-serine/L-threonine) = ADP + a [protein]-(L-serine/L-threonine) phosphate
Glossary: 3′,5′-cyclic-AMP = cAMP
Other name(s): PKA; protein kinase A; PKA catalytic (C) subunit; A kinase; ATP:protein phosphotransferase (cAMP-dependent)
Systematic name: ATP:protein Ser/Thr-phosphotransferase (3′,5′-cAMP-dependent)
Comments: This eukaryotic enzyme recognizes the sequence -Arg-Arg-X-Ser*/Thr*-Hpo, where * indicates the phosphorylated residue and Hpo indicates a hydrophobic residue.The inactive holoenzyme is a heterotetramer composed of two regulatory (R) subunits and two catalytic (C) subunits. Each R subunit occludes the active site of a C subunit and contains two binding sites for 3′,5′-cyclic-AMP (cAMP). Binding of cAMP activates the enzyme by causing conformational changes that release two free monomeric C subunits from a dimer of the R subunits, i.e. R2C2 + 4 cAMP = R2(cAMP)4 + 2 C. Activity requires phosphorylation of a conserved Thr in the activation loop (T-loop) sequence (Thr198 in human Cα; Thr224 in budding yeast Tpk2), installed by auto-phosphorylation or by the 3-phosphoinositide-dependent protein kinase-1 (PDPK1). Certain R2C2 combinations can be localized to particular subcellular regions by their association with diverse species of 'A Kinase-Anchoring Proteins' (AKAPs). The enzyme has been characterized from many organisms. Humans have three C units (Cα, Cβ, and Cγ) encoded by the paralogous genes PRKACA, PRKACB and PRKACG, respectively, and four R subunits (R1α, RIβ, RIIα and RIIβ), encoded by PKRAR1A, PKRAR1B, PKRAR2A and PKRAR2B, respectively. Yeast (Saccharomyces cerevisiae) has three C subunits (Tpk1, Tpk2, and Tpk3) encoded by the paralogous genes TPK1, TPK2 and TPK3, respectively, and a single R subunit (Bcy1) encoded by the BCY1 gene. Some validated substrates of the enzyme include cAMP-response element-binding protein (CREB), phosphorylase kinase α subunit (PHKA), and tyrosine 3-monooxygenase (TH) in mammals; Adr1, Whi3, Nej1, and Pyk1 in yeast.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 142008-29-5
References:
1.  Krebs, E.G. The Albert Lasker Medical Awards. Role of the cyclic AMP-dependent protein kinase in signal transduction. JAMA 262 (1989) 1815–1818. [DOI] [PMID: 2550680]
2.  Technikova-Dobrova, Z., Sardanelli, A.M., Speranza, F., Scacco, S., Signorile, A., Lorusso, V. and Papa, S. Cyclic adenosine monophosphate-dependent phosphorylation of mammalian mitochondrial proteins: enzyme and substrate characterization and functional role. Biochemistry 40 (2001) 13941–13947. [DOI] [PMID: 11705384]
3.  Smith, F.D., Samelson, B.K. and Scott, J.D. Discovery of cellular substrates for protein kinase A using a peptide array screening protocol. Biochem. J. 438 (2011) 103–110. [DOI] [PMID: 21644927]
4.  Broach, J.R. Nutritional control of growth and development in yeast. Genetics 192 (2012) 73–105. [DOI] [PMID: 22964838]
5.  Embogama, D.M. and Pflum, M.K. K-BILDS: a kinase substrate discovery tool. Chembiochem 18 (2017) 136–141. [DOI] [PMID: 27860220]
6.  Taylor, S.S., Wu, J., Bruystens, J.GH., Del Rio, J.C., Lu, T.W., Kornev, A.P. and Ten Eyck, L.F. From structure to the dynamic regulation of a molecular switch: A journey over 3 decades. J. Biol. Chem. 296:100746 (2021). [DOI] [PMID: 33957122]
7.  Ramms, D.J., Raimondi, F., Arang, N., Herberg, F.W., Taylor, S.S. and Gutkind, J.S. Gαs-protein kinase A (PKA) pathway signalopathies: the emerging genetic landscape and therapeutic potential of human diseases driven by aberrant Gαs-PKA signaling. Pharmacol Rev 73 (2021) 155–197. [DOI] [PMID: 34663687]
[EC 2.7.11.11 created 2005 (EC 2.7.1.37 part-incorporated 2005), modified 2022]
 
 
EC 3.2.1.215     
Accepted name: arabinogalactan exo α-(1,3)-α-D-galactosyl-(1→3)-L-arabinofuranosidase (non-reducing end)
Reaction: Hydrolysis of α-D-Galp-(1→3)-L-Araf disaccharides from non-reducing terminals in branches of type II arabinogalactan attached to proteins.
Glossary: Araf = arabinofuranose
Arap = arabinopyranose
Galp = galactopyranose
Other name(s): 3-O-α-D-galactosyl-α-L-arabinofuranosidase
Systematic name: type II arabinogalactan exo α-(1,3)-[α-D-galactosyl-(1→3)-L-arabinofuranose] hydrolase (non-reducing end)
Comments: The enzyme, characterized from the bacterium Bifidobacterium longum, specifically hydrolyses α-D-Galp-(1→3)-L-Araf disaccharides from the non-reducing terminal of arabinogalactan using an exo mode of action. It is particularly active with gum arabic arabinogalactan, a type II arabinogalactan produced by acacia trees. The enzyme can also hydrolyse β-L-Arap-(1→3)-L-Araf disaccharides, but this activity is significantly lower.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sasaki, Y., Horigome, A., Odamaki, T., Xiao, J.Z., Ishiwata, A., Ito, Y., Kitahara, K. and Fujita, K. Characterization of a novel 3-O-α-D-galactosyl-α-L-arabinofuranosidase for the assimilation of gum arabic AGP in Bifidobacterium longum subsp. longum. Appl. Environ. Microbiol. (2021) . [DOI] [PMID: 33674431]
[EC 3.2.1.215 created 2021]
 
 
EC 3.2.1.223     
Accepted name: arabinogalactan exo α-(1,3)-β-L-arabinopyranosyl-(1→3)-L-arabinofuranosidase (non-reducing end)
Reaction: Hydrolysis of β-L-Arap-(1→3)-L-Araf disaccharides from non-reducing terminals in branches of type II arabinogalactan attached to proteins.
Glossary: Araf = arabinofuranose
Arap = arabinopyranose
Other name(s): 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase; AAfase
Systematic name: type II arabinogalactan exo α-(1,3)-[β-L-arabinopyranosyl-(1→3)-L-arabinofuranose] hydrolase (non-reducing end)
Comments: The enzyme, characterized from the bacterium Bifidobacterium pseudocatenulatum, specifically hydrolyses β;-L-Arap-(1→3)-L-Araf disaccharides from the non-reducing terminal of arabinogalactan using an exo mode of action. It is active with arabinogalactan-proteins (AGPs) containing type II arabinogalactans such as gum arabic AGP and larch AGP. The enzyme can also hydrolyse α-D-Galp-(1→3)-L-Araf disaccharides (cf. EC 3.2.1.215) with a much lower activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sasaki, Y., Yanagita, M., Hashiguchi, M., Horigome, A., Xiao, J. Z., Odamaki, T., Kitahara, K. and Fujita, K. Assimilation of arabinogalactan side chains with novel 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase in Bifidobacterium pseudocatenulatum. Microbiome Res. Rep. 2:12 (2023). [DOI]
[EC 3.2.1.223 created 2023]
 
 
EC 3.4.11.26     
Accepted name: intermediate cleaving peptidase 55
Reaction: The enzyme cleaves the Pro36-Pro37 bond of cysteine desulfurase (EC 2.8.1.7) removing three amino acid residues (Tyr-Ser-Pro) from the N-terminus after cleavage by mitochondrial processing peptidase.
Other name(s): Icp55; mitochondrial intermediate cleaving peptidase 55 kDa
Comments: Icp55 removes the destabilizing N-terminal amino acid residues that are left after cleavage by the mitochondrial processing peptidase, leading to the stabilisation of the substrate. The enzyme can remove single amino acids or a short peptide, as in the case of cysteine desulfurase (EC 2.8.1.7), where three amino acids are removed.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, MEROPS, PDB
References:
1.  Naamati, A., Regev-Rudzki, N., Galperin, S., Lill, R. and Pines, O. Dual targeting of Nfs1 and discovery of its novel processing enzyme, Icp55. J. Biol. Chem. 284 (2009) 30200–30208. [DOI] [PMID: 19720832]
2.  Vogtle, F.N., Wortelkamp, S., Zahedi, R.P., Becker, D., Leidhold, C., Gevaert, K., Kellermann, J., Voos, W., Sickmann, A., Pfanner, N. and Meisinger, C. Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139 (2009) 428–439. [DOI] [PMID: 19837041]
[EC 3.4.11.26 created 2011]
 
 
EC 3.4.17.18     
Accepted name: carboxypeptidase T
Reaction: Releases a C-terminal residue, which may be hydrophobic or positively charged
Other name(s): CPT (ambiguous)
Comments: Known from Thermoactinomyces vulgaris. In peptidase family M14 (carboxypeptidase A family)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, MEROPS, PDB, CAS registry number: 89623-65-4
References:
1.  Osterman, A.L., Stepanov, V.M., Rudenskaya, G.N., Khodova, O.M., Tsaplina, I.A., Yakovleva, M.B. and Loginova, L.G. Carboxypeptidase T - an extracellular carboxypeptidase of thermophilic actinomycetes - a remote analog of animal carboxypeptidases. Biochemistry (USSR) 49 (1984) 292–301. [PMID: 6424730]
2.  Smulevitch, S.V., Osterman, A.L., Galperina, O.V., Matz, M.V., Zagnitko, O.P., Kadyrov, R.M., Tsaplina, I.A., Grishin, N.V., Chestukhina, G.G. and Stepanov, V.M. Molecular cloning and primary structure of Thermoactinomyces vulgaris carboxypeptidase T: a metalloenzyme endowed with dual substrate specificity. FEBS Lett. 291 (1991) 75–78. [DOI] [PMID: 1936254]
3.  Teplyakov, A., Polyakov, K., Obmolova, G., Strokopytov, B., Kuranova, I., Osterman, A., Grishin, N., Smulevitch, S., Zagnitko, O., Galperina, O., Matz, M. and Stepanov, V. Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris. Eur. J. Biochem. 208 (1992) 281–288. [DOI] [PMID: 1521526]
[EC 3.4.17.18 created 1993]
 
 
EC 3.6.1.12     
Accepted name: dCTP diphosphatase
Reaction: dCTP + H2O = dCMP + diphosphate
Other name(s): DCTPP1 (gene name); deoxycytidine-triphosphatase; dCTPase; dCTP pyrophosphatase; deoxycytidine triphosphatase; deoxy-CTPase
Systematic name: dCTP nucleotidohydrolase
Comments: The mammalian enzyme also displays weak activity against dTTP and dATP, but none against dGTP. Activity is highest with analogs including 5-iodo-dCTP and 5-methyl-dCTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-87-7
References:
1.  Zimmerman, S.B. and Kornberg, A. Deoxycytidine di- and triphosphate cleavage by an enzyme formed in bacteriophage-infected Escherichia coli. J. Biol. Chem. 236 (1961) 1480–1486. [PMID: 13788541]
2.  Moroz, O.V., Murzin, A.G., Makarova, K.S., Koonin, E.V., Wilson, K.S. and Galperin, M.Y. Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-α NTP pyrophosphohydrolases with potential "house-cleaning" functions. J. Mol. Biol. 347 (2005) 243–255. [DOI] [PMID: 15740738]
3.  Wu, B., Liu, Y., Zhao, Q., Liao, S., Zhang, J., Bartlam, M., Chen, W. and Rao, Z. Crystal structure of RS21-C6, involved in nucleoside triphosphate pyrophosphohydrolysis. J. Mol. Biol. 367 (2007) 1405–1412. [DOI] [PMID: 17320107]
4.  Nonaka, M., Tsuchimoto, D., Sakumi, K. and Nakabeppu, Y. Mouse RS21-C6 is a mammalian 2′-deoxycytidine 5′-triphosphate pyrophosphohydrolase that prefers 5-iodocytosine. FEBS J. 276 (2009) 1654–1666. [DOI] [PMID: 19220460]
5.  Requena, C.E., Perez-Moreno, G., Ruiz-Perez, L.M., Vidal, A.E. and Gonzalez-Pacanowska, D. The NTP pyrophosphatase DCTPP1 contributes to the homoeostasis and cleansing of the dNTP pool in human cells. Biochem. J. 459 (2014) 171–180. [DOI] [PMID: 24467396]
[EC 3.6.1.12 created 1965]
 
 
EC 6.3.1.12     
Accepted name: D-aspartate ligase
Reaction: ATP + D-aspartate + [β-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)]n = [β-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-6-N-(β-D-Asp)-L-Lys-D-Ala-D-Ala)]n + ADP + phosphate
For diagram of reaction, click here
Other name(s): Aslfm; UDP-MurNAc-pentapeptide:D-aspartate ligase; D-aspartic acid-activating enzyme
Systematic name: D-aspartate:[β-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)]n ligase (ADP-forming)
Comments: This enzyme forms part of the peptidoglycan assembly pathway of Gram-positive bacteria grown in medium containing D-Asp. Normally, the side chains the acylate the 6-amino group of the L-lysine residue contain L-Ala-L-Ala but these amino acids are replaced by D-Asp when D-Asp is included in the medium. Hybrid chains containing L-Ala-D-Asp, L-Ala-L-Ala-D-Asp or D-Asp-L-Ala are not formed [4]. The enzyme belongs in the ATP-grasp protein superfamily [3,4]. The enzyme is highly specific for D-aspartate, as L-aspartate, D-glutamate, D-alanine, D-iso-asparagine and D-malic acid are not substrates [4]. In Enterococcus faecium, the substrate D-aspartate is produced by EC 5.1.1.13, aspartate racemase [4]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Staudenbauer, W. and Strominger, J.L. Activation of D-aspartic acid for incorporation into peptidoglycan. J. Biol. Chem. 247 (1972) 5095–5102. [PMID: 4262567]
2.  Staudenbauer, W., Willoughby, E. and Strominger, J.L. Further studies of the D-aspartic acid-activating enzyme of Streptococcus faecalis and its attachment to the membrane. J. Biol. Chem. 247 (1972) 5289–5296. [PMID: 4626717]
3.  Galperin, M.Y. and Koonin, E.V. A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Protein Sci. 6 (1997) 2639–2643. [DOI] [PMID: 9416615]
4.  Bellais, S., Arthur, M., Dubost, L., Hugonnet, J.E., Gutmann, L., van Heijenoort, J., Legrand, R., Brouard, J.P., Rice, L. and Mainardi, J.L. Aslfm, the D-aspartate ligase responsible for the addition of D-aspartic acid onto the peptidoglycan precursor of Enterococcus faecium. J. Biol. Chem. 281 (2006) 11586–11594. [DOI] [PMID: 16510449]
[EC 6.3.1.12 created 2006]
 
 


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