Enzyme Nomenclature

Continued from EC 3.2.1.151 to 3.2.1.208

EC 3.2.2 and EC 3.2.3

Sections

EC 3.2.2 Hydrolysing N-Glycosyl Compounds
EC 3.2.3 Hydrolysing S-Glycosyl Compounds


EC 3.2.2 Hydrolysing N-Glycosyl Compounds

Contents

EC 3.2.2.1 purine nucleosidase
EC 3.2.2.2 inosine nucleosidase
EC 3.2.2.3 uridine nucleosidase
EC 3.2.2.4 AMP nucleosidase
EC 3.2.2.5 NAD+ glycohydrolase
EC 3.2.2.6 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
EC 3.2.2.7 adenosine nucleosidase
EC 3.2.2.8 ribosylpyrimidine nucleosidase
EC 3.2.2.9 adenosylhomocysteine nucleosidase
EC 3.2.2.10 pyrimidine-5'-nucleotide nucleosidase
EC 3.2.2.11 β-aspartyl-N-acetylglucosaminidase
EC 3.2.2.12 inosinate nucleosidase
EC 3.2.2.13 1-methyladenosine nucleosidase
EC 3.2.2.14 NMN nucleosidase
EC 3.2.2.15 DNA-deoxyinosine glycosylase
EC 3.2.2.16 methylthioadenosine nucleosidase
EC 3.2.2.17 deoxyribodipyrimidine endonucleosidase
EC 3.2.2.18 deleted, included in EC 3.5.1.52
EC 3.2.2.19 ADP-ribosylarginine hydrolase
EC 3.2.2.20 DNA-3-methyladenine glycosylase I
EC 3.2.2.21 DNA-3-methyladenine glycosylase II
EC 3.2.2.22 rRNA N-glycosylase
EC 3.2.2.23 DNA-formamidopyrimidine glycosylase
EC 3.2.2.24 ADP-ribosyl-[dinitrogen reductase] hydrolase
EC 3.2.2.25 N-methyl nucleosidase
EC 3.2.2.26 futalosine hydrolase
EC 3.2.2.27 uracil-DNA glycosylase
EC 3.2.2.28 double-stranded uracil-DNA glycosylase
EC 3.2.2.29 thymine-DNA glycosylase
EC 3.2.2.30 aminodeoxyfutalosine nucleosidase
EC 3.2.2.31 adenine glycosylase


Entries

EC 3.2.2.1

Accepted name: purine nucleosidase

Reaction: a purine nucleoside + H2O = D-ribose + a purine base

Other name(s): nucleosidase (misleading); purine β-ribosidase; purine nucleoside hydrolase; purine ribonucleosidase; ribonucleoside hydrolase (misleading); nucleoside hydrolase (misleading); N-ribosyl purine ribohydrolase; nucleosidase g; N-D-ribosylpurine ribohydrolase; inosine-adenosine-guanosine preferring nucleoside hydrolase; purine-specific nucleoside N-ribohydrolase; IAG-nucleoside hydrolase; IAG-NH

Systematic name: purine-nucleoside ribohydrolase

Comments: The enzyme from the bacterium Ochrobactrum anthropi specifically catalyses the irreversible N-riboside hydrolysis of purine nucleosides. Pyrimidine nucleosides, purine and pyrimidine nucleotides, NAD+, NADP+ and nicotinaminde mononucleotide are not substrates [6].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9025-44-9

References:

1. Heppel, L.A. and Hilmoe, R.J. Phosphorolysis and hydrolysis of purine ribosides from yeast. J. Biol. Chem. 198 (1952) 683-694. [PMID: 12999785]

2. Kalckar, H.M. Biosynthetic aspects of nucleosides and nucleic acids. Pubbl. Staz. Zool. (Napoli) 23 (1951) 87-103.

3. Takagi, Y. and Horecker, B.L. Purification and properties of a bacterial riboside hydrolyase. J. Biol. Chem. 225 (1956) 77-86. [PMID: 13416219]

4. Tarr, H.L.A. Fish muscle riboside hydrolases. Biochem. J. 59 (1955) 386-391. [PMID: 14363106]

5. Parkin, D.W. Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism. J. Biol. Chem. 271 (1996) 21713-21719. [PMID: 8702965]

6. Ogawa, J., Takeda, S., Xie, S.X., Hatanaka, H., Ashikari, T., Amachi, T. and Shimizu, S. Purification, characterization, and gene cloning of purine nucleosidase from Ochrobactrum anthropi. Appl. Environ. Microbiol. 67 (2001) 1783-1787. [PMID: 11282633]

7. Versées, W., Decanniere, K., Van Holsbeke, E., Devroede, N. and Steyaert, J. Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax. J. Biol. Chem. 277 (2002) 15938-15946. [PMID: 11854281]

8. Mazumder-Shivakumar, D. and Bruice, T.C. Computational study of IAG-nucleoside hydrolase: determination of the preferred ground state conformation and the role of active site residues. Biochemistry 44 (2005) 7805-7817. [PMID: 15909995]

[EC 3.2.2.1 created 1961, modified 2006, modified 2011]

EC 3.2.2.2

Accepted name: inosine nucleosidase

Reaction: inosine + H2O = D-ribose + hypoxanthine

Other name(s): inosinase; inosine-guanosine nucleosidase

Systematic name: inosine ribohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9030-95-9

References:

1. Koch, A.L. Some enzymes of nucleoside metabolism of Escherichia coli. J. Biol. Chem. 223 (1956) 535-549.

2. Tarr, H.L.A. Fish muscle riboside hydrolases. Biochem. J. 59 (1955) 386-391.

[EC 3.2.2.2 created 1961]

EC 3.2.2.3

Accepted name: uridine nucleosidase

Reaction: uridine + H2O = D-ribose + uracil

Other name(s): uridine hydrolase

Systematic name: uridine ribohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9025-47-2

References:

1. Carter, C.E. Partial purification of a non-phosphorylytic uridine nucleosidase from yeast. J. Am. Chem. Soc. 73 (1951) 1508-1510.

[EC 3.2.2.3 created 1961]

EC 3.2.2.4

Accepted name: AMP nucleosidase

Reaction: AMP + H2O = D-ribose 5-phosphate + adenine

Other name(s): adenylate nucleosidase; adenosine monophosphate nucleosidase

Systematic name: AMP phosphoribohydrolase

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9025-45-0

References:

1. Hurwitz, J., Heppel, L.A. and Horecker, B.L. The enzymatic cleavage of adenylic acid to adenine and ribose 5-phosphate. J. Biol. Chem. 226 (1957) 525-540.

[EC 3.2.2.4 created 1961]

EC 3.2.2.5

Accepted name: NAD+ glycohydrolase

Reaction: NAD+ + H2O = ADP-D-ribose + nicotinamide

Glossary: ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)

Other name(s): NAD glycohydrolase; nicotinamide adenine dinucleotide glycohydrolase; β-NAD+ glycohydrolase; DPNase (ambiguous); NAD hydrolase (ambiguous); diphosphopyridine nucleosidase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD nucleosidase (ambiguous); DPN hydrolase (ambiguous); NADase (ambiguous); nga (gene name)

Systematic name: NAD+ glycohydrolase

Comments: This enzyme catalyses the hydrolysis of NAD+, without associated ADP-ribosyl cyclase activities (unlike the metazoan enzyme EC 3.2.2.6, bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase). The enzyme from Group A streptococci has been implicated in the pathogenesis of diseases such as streptococcal toxic shock-like syndrome (STSS) and necrotizing fasciitis. The enzyme from the venom of the snake Agkistrodon acutus also catalyses EC 3.6.1.5, apyrase [3].

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9025-46-1

References:

1. Fehrenbach, F.J. Reinigung und Kristallisation der NAD-Glykohydrolase aus C-Streptokokken. Eur. J. Biochem. 18 (1971) 94-102. [PMID: 4322210]

2. Grushoff, P.S., Shany, S. and Bernheimer, A.W. Purification and properties of streptococcal nicotinamide adenine dinucleotide glycohydrolase. J. Bacteriol. 122 (1975) 599-605. [PMID: 236282]

3. Zhang, L., Xu, X., Luo, Z., Shen, D. and Wu, H. Identification of an unusual AT(D)Pase-like activity in multifunctional NAD glycohydrolase from the venom of Agkistrodon acutus. Biochimie 91 (2009) 240-251. [PMID: 18952139]

4. Ghosh, J., Anderson, P.J., Chandrasekaran, S. and Caparon, M.G. Characterization of Streptococcus pyogenes β-NAD+ glycohydrolase: re-evaluation of enzymatic properties associated with pathogenesis. J. Biol. Chem. 285 (2010) 5683-5694. [PMID: 20018886]

5. Smith, C.L., Ghosh, J., Elam, J.S., Pinkner, J.S., Hultgren, S.J., Caparon, M.G. and Ellenberger, T. Structural basis of Streptococcus pyogenes immunity to its NAD+ glycohydrolase toxin. Structure 19 (2011) 192-202. [PMID: 21300288]

[EC 3.2.2.5 created 1961, modified 2013]

EC 3.2.2.6

Accepted name: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

Reaction: NAD+ + H2O = ADP-D-ribose + nicotinamide (overall reaction)
(1a) NAD+ = cyclic ADP-ribose + nicotinamide
(1b) cyclic ADP-ribose + H2O = ADP-D-ribose

For diagram of reaction click here.

Glossary: ADP-D-ribose = adenosine 5'-(5-deoxy-D-ribofuranos-5-yl diphosphate)
cyclic ADP-ribose = N1-(β-D-ribosyl)adenosine 5'(P1),5''(P2)-cyclic diphosphate

Other name(s): NAD+ nucleosidase; NADase (ambiguous); DPNase (ambiguous); DPN hydrolase (ambiguous); NAD hydrolase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD glycohydrolase (misleading); NAD nucleosidase (ambiguous); nicotinamide adenine dinucleotide glycohydrolase (misleading); CD38 (gene name); BST1 (gene name)

Systematic name: NAD+ glycohydrolase (cyclic ADP-ribose-forming)

Comments: This multiunctional enzyme catalyses both the synthesis and hydrolysis of cyclic ADP-ribose, a calcium messenger that can mobilize intracellular Ca2+ stores and activate Ca2+ influx to regulate a wide range of physiological processes. In addition, the enzyme also catalyses EC 2.4.99.20, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase. It is also able to act on β-nicotinamide D-ribonucleotide. cf. EC 3.2.2.5, NAD+ glycohydrolase.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9032-65-9

References:

1. Imai, T. Purification and characterization of a pyridine nucleotide glycohydrolase from rabbit spleen. J. Biochem. 106 (1989) 928937. [PMID: 2613697]

2. Howard, M., Grimaldi, J.C., Bazan, J.F., Lund, F.E., Santos-Argumedo, L., Parkhouse, R.M., Walseth, T.F. and Lee, H.C. Formation and hydrolysis of cyclic ADP-ribose catalyzed by lymphocyte antigen CD38. Science 262 (1993) 1056-1059. [PMID: 8235624]

3. Takasawa, S., Tohgo, A., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Yonekura, H. and Okamoto, H. Synthesis and hydrolysis of cyclic ADP-ribose by human leukocyte antigen CD38 and inhibition of the hydrolysis by ATP. J. Biol. Chem. 268 (1993) 26052-26054. [PMID: 8253715]

4. Tohgo, A., Takasawa, S., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Furuya, Y., Yonekura, H. and Okamoto, H. Essential cysteine residues for cyclic ADP-ribose synthesis and hydrolysis by CD38. J. Biol. Chem. 269 (1994) 28555-28557. [PMID: 7961800]

5. Fryxell, K.B., O'Donoghue, K., Graeff, R.M., Lee, H.C. and Branton, W.D. Functional expression of soluble forms of human CD38 in Escherichia coli and Pichia pastoris. Protein Expr. Purif. 6 (1995) 329-336. [PMID: 7663169]

6. Yamamoto-Katayama, S., Ariyoshi, M., Ishihara, K., Hirano, T., Jingami, H. and Morikawa, K. Crystallographic studies on human BST-1/CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities. J. Mol. Biol. 316 (2002) 711-723. [PMID: 11866528]

7. Liu, Q., Kriksunov, I.A., Graeff, R., Munshi, C., Lee, H.C. and Hao, Q. Crystal structure of human CD38 extracellular domain. Structure 13 (2005) 1331-1339. [PMID: 16154090]

[EC 3.2.2.6 created 1961, modified 2004, modified 2014]

EC 3.2.2.7

Accepted name: adenosine nucleosidase

Reaction: adenosine + H2O = D-ribose + adenine

Other name(s): adenosinase; N-ribosyladenine ribohydrolase; adenosine hydrolase; ANase

Systematic name: adenosine ribohydrolase

Comments: Also acts on adenosine N-oxide.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9075-41-6

References:

1. Mazelis, M. and Creveling, R.K. An adenosine hydrolase from brussels sprouts. J. Biol. Chem. 238 (1963) 3358-3361.

[EC 3.2.2.7 created 1972]

EC 3.2.2.8

Accepted name: ribosylpyrimidine nucleosidase

Reaction: a pyrimidine nucleoside + H2O = D-ribose + a pyrimidine base

Other name(s): N-ribosylpyrimidine nucleosidase; pyrimidine nucleosidase; N-ribosylpyrimidine ribohydrolase; pyrimidine nucleoside hydrolase; RihB; YeiK; nucleoside ribohydrolase

Systematic name: pyrimidine-nucleoside ribohydrolase

Comments: Also hydrolyses purine D-ribonucleosides, but more slowly. 2'-, 3'- and 5'-deoxynucleosides are not substrates [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37288-60-1

References:

1. Terada, M., Tatibana, M. and Hayaishi, O. Preparation and properties of nucleoside hydrolase from Pseudomonas fluorescens. J. Biol. Chem. 242 (1967) 5578-5585. [PMID: 12325375]

2. Petersen, C. and Møller, L.B. The RihA, RihB, and RihC ribonucleoside hydrolases of Escherichia coli. Substrate specificity, gene expression, and regulation. J. Biol. Chem. 276 (2001) 884-894. [PMID: 11027694]

3. Giabbai, B. and Degano, M. Cloning, purification, crystallization and X-ray analysis of the Escherichia coli pyrimidine nucleoside hydrolase YeiK. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 524-527. [PMID: 14993681]

4. Giabbai, B. and Degano, M. Crystal structure to 1.7 Å of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy. Structure 12 (2004) 739-749. [PMID: 15130467]

[EC 3.2.2.8 created 1972]

EC 3.2.2.9

Accepted name: adenosylhomocysteine nucleosidase

Reaction: S-adenosyl-L-homocysteine + H2O = S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine

For diagram click here or here.

Other name(s): S-adenosylhomocysteine hydrolase (ambiguous); S-adenosylhomocysteine nucleosidase; 5'-methyladenosine nucleosidase; S-adenosylhomocysteine/5'-methylthioadenosine nucleosidase; AdoHcy/MTA nucleosidase

Systematic name: S-adenosyl-L-homocysteine homocysteinylribohydrolase

Comments: Also acts on S-methyl-5'-thioadenosine to give adenine and S-methyl-5-thioribose (cf. EC 3.2.2.16, methylthioadenosine nucleosidase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9055-10-1

References:

1. Duerre, J.A. A hydrolytic nucleosidase acting on S-adenosylhomocysteine and on 5-methylthioadenosine. J. Biol. Chem. 237 (1962) 3737-3741.

2. Ferro, A.J., Barrett, A. and Shapiro, S.K. Kinetic properties and the effect of substrate analogues on 5'-methylthioadenosine nucleosidase from Escherichia coli. Biochim. Biophys. Acta 438 (1976) 487-494. [PMID: 782530]

[EC 3.2.2.9 created 1972, modified 2004]

EC 3.2.2.10

Accepted name: pyrimidine-5'-nucleotide nucleosidase

Reaction: a pyrimidine 5'-nucleotide + H2O = D-ribose 5-phosphate + a pyrimidine base

Other name(s): pyrimidine nucleotide N-ribosidase; Pyr5N

Systematic name: pyrimidine-5'-nucleotide phosphoribo(deoxyribo)hydrolase

Comments: Also acts on dUMP, dTMP and dCMP.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9023-31-8

References:

1. Imada, A. Degradation of pyrimidine nucleotides by enzyme systems of Streptomyces. II. Pyrimidine 5'-nucleotide phosphoribo(deoxyribo) hydrolase of Streptomyces virginiae. J. Gen. Appl. Microbiol. 13 (1967) 267-278.

2. Imada, A., Kuno, M. and Igarasi, S. Degradation of pyrimidine nucleotides by enzyme systems of Streptomyces. I. Ribose-5-phosphate formation from pyrimidine nucleotides. J. Gen. Appl. Microbiol. 13 (1967) 255-265.

[EC 3.2.2.10 created 1972]

EC 3.2.2.11

Accepted name: β-aspartyl-N-acetylglucosaminidase

Reaction: 1-β-aspartyl-N-acetyl-D-glucosaminylamine + H2O = L-asparagine + N-acetyl-D-glucosamine

Other name(s): β-aspartylacetylglucosaminidase

Systematic name: 1-β-aspartyl-N-acetyl-D-glucosaminylamine L-asparaginohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9027-31-0

References:

1. Eylar, E.H. and Murakami, M. β-Aspartyl-N-acetylglucosaminidase from epididymis. Methods Enzymol. 8 (1966) 597-600.

[EC 3.2.2.11 created 1972]

EC 3.2.2.12

Accepted name: inosinate nucleosidase

Reaction: IMP + H2O = D-ribose 5-phosphate + hypoxanthine

For diagram click here.

Glossary: IMP = inosine 5'-phosphate

Other name(s): 5'-inosinate phosphoribohydrolase

Systematic name: IMP phosphoribohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37288-61-2

References:

1. Kuninaka, A. 5'-Inosinic acid-N-ribosidase in Aspergillus. Koso Kagaka Shinojiumu 12 (1957) 65-69.

[EC 3.2.2.12 created 1972]

EC 3.2.2.13

Accepted name: 1-methyladenosine nucleosidase

Reaction: 1-methyladenosine + H2O = 1-methyladenine + D-ribose

Other name(s): 1-methyladenosine hydrolase

Systematic name: 1-methyladenosine ribohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37367-71-8

References:

1. Tarr, H.L.A. 1-Methyladenosine hydrolase of starfish (Pisaster ochraceous). J. Fish Res. Board Can. 30 (1973) 1861-1866.

[EC 3.2.2.13 created 1976]

EC 3.2.2.14

Accepted name: NMN nucleosidase

Reaction: nicotinamide β-D-ribonucleotide + H2O = D-ribose 5-phosphate + nicotinamide

Other name(s): NMNase; nicotinamide mononucleotide nucleosidase; nicotinamide mononucleotidase; NMN glycohydrolase; NMNGhase

Systematic name: nicotinamide-nucleotide phosphoribohydrolase

Comments: The enzyme is thought to participate in an NAD+-salvage pathway. In eukaryotic organisms this activity has been attributed to EC 3.2.2.6, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37237-49-3

References:

1. Andreoli, A.J., Okita, T.W., Bloom, R. and Grover, T.A. The pyridine nucleotide cycle: presence of a nicotinamide mononucleotide-specific glycohydrolase in Escherichia coli. Biochem. Biophys. Res. Commun. 49 (1972) 264-269. [PMID: 4342726]

2. Imai, T. Isolation and properties of a glycohydrolase specific for nicotinamide mononucleotide from Azotobacter vinelandii. J. Biochem. 85 (1979) 887899. [PMID: 457634]

3. Imai, T. Properties of allosteric nicotinamide mononucleotide glycohydrolase from Azotobacter vinelandii: activation and inhibition. J. Biochem. 101 (1987) 163173. [PMID: 3571198]

[EC 3.2.2.14 created 1976]

EC 3.2.2.15

Accepted name: DNA-deoxyinosine glycosylase

Reaction: Hydrolyses DNA and polynucleotides, releasing free hypoxanthine

Other name(s): DNA(hypoxanthine) glycohydrolase; deoxyribonucleic acid glycosylase; hypoxanthine-DNA glycosylase

Systematic name: DNA-deoxyinosine deoxyribohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 68247-62-1

References:

1. Karran, P. and Lindahl, T. Enzymatic excision of free hypoxanthine from polydeoxynucleotides and DNA containing deoxyinosine monophosphate residues. J. Biol. Chem. 253 (1978) 5877-5879. [PMID: 98523]

[EC 3.2.2.15 created 1980, modified 1982, modified 2000]

EC 3.2.2.16

Accepted name: methylthioadenosine nucleosidase

Reaction: S-methyl-5'-thioadenosine + H2O = S-methyl-5-thio-D-ribose + adenine

For diagram click here.

Other name(s): 5'-methylthioadenosine nucleosidase; MTA nucleosidase; MeSAdo nucleosidase; methylthioadenosine methylthioribohydrolase

Systematic name: S-methyl-5'-thioadenosine adeninehyrolase

Comments: Does not act on S-adenosylhomocysteine. cf. EC 3.2.2.9 adenosylhomocysteine nucleosidase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 50812-28-7

References:

1. Guranowski, A.B., Chiang, P.K. and Cantoni, G.L. 5'-Methylthioadenosine nucleosidase. Purification and characterization of the enzyme from Lupinus luteus seeds. Eur. J. Biochem. 114 (1981) 293-299. [PMID: 6783408]

[EC 3.2.2.16 created 1983, modified 2004]

EC 3.2.2.17

Accepted name: deoxyribodipyrimidine endonucleosidase

Reaction: Cleaves the N-glycosidic bond between the 5'-pyrimidine residue in cyclobutadipyrimidine (in DNA) and the corresponding deoxy-D-ribose residue

Other name(s): pyrimidine dimer DNA-glycosylase; endonuclease V; deoxyribonucleate pyrimidine dimer glycosidase; pyrimidine dimer DNA glycosylase; T4-induced UV endonuclease; PD-DNA glycosylase

Systematic name: deoxy-D-ribocyclobutadipyrimidine polynucleotidodeoxyribohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 75302-33-9

References:

1. Haseltine, W.A., Gordon, L.K., Lindan, C.P., Grafstrom, R.H., Shaper, N.L. and Grossman, L. Cleavage of pyrimidine dimers in specific DNA sequences by a pyrimidine dimer DNA-glycosylase of M. luteus. Nature 285 (1980) 634-641. [PMID: 6248789]

[EC 3.2.2.17 created 1983]

[EC 3.2.2.18 Deleted entry: glycopeptide N-glycosidase. Now included with EC 3.5.1.52 N4-(β-N-acetylglucosaminyl)-L-asparaginase (EC 3.2.2.18 created 1984, deleted 1989)]

EC 3.2.2.19

Accepted name: [protein ADP-ribosylarginine] hydrolase

Reaction: (1) protein-Nω-(ADP-D-ribosyl)-L-arginine + H2O = ADP-D-ribose + protein-L-arginine
(2) Nω-(ADP-D-ribosyl)-L-arginine + H2O = ADP-ribose + L-arginine

Other name(s): ADP-ribose-L-arginine cleavage enzyme; ADP-ribosylarginine hydrolase; Nω-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase

Systematic name: protein-Nω-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase

Comments: The enzyme will remove ADP-D-ribose from arginine residues in ADP-ribosylated proteins.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 98668-52-1

References:

1. Moss, J., Jacobson, M.K. and Stanley, S.J. Reversibility of arginine-specific mono(ADP-ribosyl)ation: identification in erythrocytes of an ADP-ribose-L-arginine cleavage enzyme. Proc. Natl. Acad. Sci. USA 82 (1985) 5603-5607. [PMID: 2994036]

2. Moss, J., Stanley, S.J., Nightingale, M.S., Murtagh, J.J., Jr., Monaco, L., Mishima, K., Chen, H.C., Williamson, K.C. and Tsai, S.C. Molecular and immunological characterization of ADP-ribosylarginine hydrolases. J. Biol. Chem. 267 (1992) 10481-10488. [PMID: 1375222]

3. Konczalik, P. and Moss, J. Identification of critical, conserved vicinal aspartate residues in mammalian and bacterial ADP-ribosylarginine hydrolases. J. Biol. Chem. 274 (1999) 16736-16740. [PMID: 10358013]

4. Takada, T., Iida, K. and Moss, J. Cloning and site-directed mutagenesis of human ADP-ribosylarginine hydrolase. J. Biol. Chem. 268 (1993) 17837-17843 [PMID: 8349667]

5. Ohno, T., Tsuchiya, M., Osago, H., Hara, N., Jidoi, J. and Shimoyama, M. Detection of arginine-ADP-ribosylated protein using recombinant ADP-ribosylarginine hydrolase. Anal. Biochem. 10 (1995) 115-122 [PMID: 8678289]

[EC 3.2.2.19 created 1989, modified 2004]

EC 3.2.2.20

Accepted name: DNA-3-methyladenine glycosylase I

Reaction: Hydrolysis of alkylated DNA, releasing 3-methyladenine

Other name(s): deoxyribonucleate 3-methyladenine glycosidase I; 3-methyladenine DNA glycosylase I; DNA-3-methyladenine glycosidase I

Systematic name: alkylated-DNA glycohydrolase (releasing methyladenine and methylguanine)

Comments: Involved in the removal of alkylated bases from DNA in Escherichia coli (cf. EC 2.1.1.63 methylated-DNA—[protein]-cysteine S-methyltransferase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 89287-37-6

References:

1. Evensen, G. and Seeberg, E. Adaptation to alkylation resistance involves the induction of a DNA glycosylase. Nature 296 (1982) 773-775. [PMID: 7040984]

2. Karran, P., Hjelmgren, T. and Lindahl, T. Induction of a DNA glycosylase for N-methylated purines is part of the adaptive response to alkylating agents. Nature 296 (1982) 770-773. [PMID: 7040983]

3. Thomas, L., Yang, C.-H. and Goldthwait, D.A. Two DNA glycosylases in Escherichia coli which release primarily 3-methyladenine. Biochemistry 21 (1982) 1162-1169. [PMID: 7041972]

[EC 3.2.2.20 created 1990, modified 2000]

EC 3.2.2.21

Accepted name: DNA-3-methyladenine glycosylase II

Reaction: Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine

Other name(s): deoxyribonucleate 3-methyladenine glycosidase II; 3-methyladenine DNA glycosylase II; DNA-3-methyladenine glycosidase II; AlkA

Systematic name: alkylated-DNA glycohydrolase (releasing methyladenine and methylguanine)

Comments: Involved in the removal of alkylated bases from DNA in Escherichia coli (cf. EC 2.1.1.63 methylated-DNA—[protein]-cysteine S-methyltransferase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 89287-38-7

References:

1. Evensen, G. and Seeberg, E. Adaptation to alkylation resistance involves the induction of a DNA glycosylase. Nature 296 (1982) 773-775. [PMID: 7040984]

2. Karran, P., Hjelmgren, T. and Lindahl, T. Induction of a DNA glycosylase for N-methylated purines is part of the adaptive response to alkylating agents. Nature 296 (1982) 770-773. [PMID: 7040983]

3. Riazuddin, S. and Lindahl, T. Properties of 3-methyladenine-DNA glycosylase from Escherichia coli. Biochemistry 17 (1978) 2110-2118. [PMID: 352392]

4. Thomas, L., Yang, C.-H. and Goldthwait, D.A. Two DNA glycosylases in Escherichia coli which release primarily 3-methyladenine. Biochemistry 21 (1982) 1162-1169. [PMID: 7041972]

[EC 3.2.2.21 created 1990, modified 2000]

EC 3.2.2.22

Accepted name: rRNA N-glycosylase

Reaction: Hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes

Other name(s): ribosomal ribonucleate N-glycosidase; nigrin b; RNA N-glycosidase; rRNA N-glycosidase; ricin; momorcochin-S; Mirabilis antiviral protein; momorcochin-S; gelonin; saporins

Systematic name: rRNA N-glycohydrolase

Comments: Ricin A-chain and related toxins show this activity. Naked rRNA is attacked more slowly than rRNA in intact ribosomes. Naked rRNA from Escherichia coli is cleaved at a corresponding position.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 113756-12-0

References:

1. Endo, Y. and Tsurugi, K. The RNA N-glycosidase activity of ricin A-chain. The characteristics of the enzymatic activity of ricin A-chain with ribosomes and with rRNA. J. Biol. Chem. 263 (1988) 8735-8739. [PMID: 3288622]

[EC 3.2.2.22 created 1990, modified 2000]

EC 3.2.2.23

Accepted name: DNA-formamidopyrimidine glycosylase

Reaction: Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine

Other name(s): Fapy-DNA glycosylase; deoxyribonucleate glycosidase; 2,6-diamino-4-hydroxy-5N-formamidopyrimidine-DNA glycosylase; 2,6-diamino-4-hydroxy-5(N-methyl)formamidopyrimidine-DNA glycosylase; formamidopyrimidine-DNA glycosylase; DNA-formamidopyrimidine glycosidase; Fpg protein

Systematic name: DNA glycohydrolase [2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide releasing]

Comments: May play a significant role in processes leading to recovery from mutagenesis and/or cell death by alkylating agents. Also involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 78783-53-6

References:

1. Boiteux, S., O'Connor, T.R. and Laval J. Formamidopyrimidine-DNA glycosylase of Escherichia coli: cloning and sequencing of the fpg structural gene and overproduction of the protein. EMBO J. 6 (1987) 3177-3183. [PMID: 3319582]

[EC 3.2.2.23 created 1990, modified 2000]

EC 3.2.2.24

Accepted name: ADP-ribosyl-[dinitrogen reductase] hydrolase

Reaction: [dinitrogen reductase]-Nω-α-(ADP-D-ribosyl)-L-arginine = ADP-D-ribose + [dinitrogen reductase]-L-arginine

Other name(s): azoferredoxin glycosidase; azoferredoxin-activating enzymes; dinitrogenase reductase-activating glycohydrolase; ADP-ribosyl glycohydrolase; draG (gene name)

Systematic name: ADP-D-ribosyl-[dinitrogen reductase] ADP-ribosylhydrolase

Comments: The enzyme restores the activity of EC 1.18.6.1, nitrogenase, by catalysing the removal of ADP-ribose from an arginine residue of the dinitrogenase reductase component of nitrogenase. This activity occurs only when the nitrogenase product, ammonium, is not available. The combined activity of this enzyme and EC 2.4.2.37, NAD+-dinitrogen-reductase ADP-D-ribosyltransferase, controls the level of activity of nitrogenase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 125626-63-3

References:

1. Fitzmaurice, W.P., Saari, L.L., Lowery, R.G., Ludden, P.W. and Roberts, G.P. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Mol. Gen. Genet. 218 (1989) 340-347. [PMID: 2506427]

2. Li, X.D., Huergo, L.F., Gasperina, A., Pedrosa, F.O., Merrick, M. and Winkler, F.K. Crystal structure of dinitrogenase reductase-activating glycohydrolase (DraG) reveals conservation in the ADP-ribosylhydrolase fold and specific features in the ADP-ribose-binding pocket. J. Mol. Biol. 390 (2009) 737-746. [PMID: 19477184]

3. Berthold, C.L., Wang, H., Nordlund, S. and Hogbom, M. Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG. Proc. Natl. Acad. Sci. USA 106 (2009) 14247-14252. [PMID: 19706507]

[EC 3.2.2.24 created 1992]

EC 3.2.2.25

Accepted name: N-methyl nucleosidase

Reaction: 7-methylxanthosine + H2O = 7-methylxanthine + D-ribose

For diagram of reaction click here

Other name(s): 7-methylxanthosine nucleosidase; N-MeNase; N-methyl nucleoside hydrolase; methylpurine nucleosidase

Systematic name: 7-methylxanthosine ribohydrolase

Comments: The enzyme preferentially hydrolyses 3- and 7-methylpurine nucleosides, such as 3-methylxanthosine, 3-methyladenosine and 7-methylguanosine. Hydrolysis of 7-methylxanthosine to form 7-methylxanthine is the second step in the caffeine-biosynthesis pathway.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1.Negishi, O., Ozawa, T. and Imagawa, H. N-Methyl nucleosidase from tea leaves. Agric. Biol. Chem. 52 (1988) 169-175.

[EC 3.2.2.25 created 2007]

EC 3.2.2.26

Accepted name: futalosine hydrolase

Reaction: futalosine + H2O = dehypoxanthine futalosine + hypoxanthine

For diagram of reaction click here.

Glossary: futalosine = 3-(3-((3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9(6H)-yl)tetrahydrofuran-2-yl)propanoyl)benzoate
dehypoxanthine futalosine = 7-(3-carboxyphenyl)-D-ribo-7-dehydro-5,6-dideoxyheptose

Other name(s): futalosine nucleosidase; MqnB

Systematic name: futalosine ribohydrolase

Comments: This enzyme, which is specific for futalosine, catalyses the second step of a novel menaquinone biosynthetic pathway that is found in some prokaryotes.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670-1673. [PMID: 18801996]

[EC 3.2.2.26 created 2008]

EC 3.2.2.27

Accepted name: uracil-DNA glycosylase

Reaction: Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil

Other name(s): UdgB (ambiguous); uracil-DNA N-glycosylase; UDG (ambiguous); uracil DNA glycohydrolase

Systematic name: uracil-DNA deoxyribohydrolase (uracil-releasing)

Comments: Uracil-DNA glycosylases are widespread enzymes that are found in all living organisms. EC 3.2.2.27 and double-stranded uracil-DNA glycosylase (EC 3.2.2.28) form a central part of the DNA-repair machinery since they initiate the DNA base-excision repair pathway by hydrolysing the N-glycosidic bond between uracil and the deoxyribose sugar thereby catalysing the removal of mis-incorporated uracil from DNA.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Lee, M.S., Kim, G.A., Seo, M.S., Lee, J.H. and Kwon, S.T. Characterization of heat-labile uracil-DNA glycosylase from Psychrobacter sp. HJ147 and its application to the polymerase chain reaction. Biotechnol. Appl. Biochem. 52 (2009) 167-175. [PMID: 18412541]

2. Kim, G.A., Lee, M.S., Sun, Y., Lee, B.D., Lee, J.I., Lee, J.H. and Kwon, S.T. Characterization of cold-active uracil-DNA glycosylase from Bacillus sp. HJ171 and its use for contamination control in PCR. Appl. Microbiol. Biotechnol. 80 (2008) 785-794. [PMID: 18626641]

3. Parikh, S.S., Putnam, C.D. and Tainer, J.A. Lessons learned from structural results on uracil-DNA glycosylase. Mutat Res 460 (2000) 183-199. [PMID: 10946228]

4. Stivers, J.T. and Drohat, A.C. Uracil DNA glycosylase: insights from a master catalyst. Arch. Biochem. Biophys. 396 (2001) 1-9. [PMID: 11716455]

[EC 3.2.2.27 created 2009]

EC 3.2.2.28

Accepted name: double-stranded uracil-DNA glycosylase

Reaction: Specifically hydrolyzes mismatched double-stranded DNA and polynucleotides, releasing free uracil

Other name(s): Mug; double-strand uracil-DNA glycosylase; Dug; dsUDG; double-stranded DNA specific UDG; dsDNA specific UDG; UdgB (ambiguous); G:T/U mismatch-specific DNA glycosylase; UDG (ambiguous)

Systematic name: uracil-double-stranded DNA deoxyribohydrolase (uracil-releasing)

Comments: No activity on DNA containing a T/G mispair or single-stranded DNA containing either a site-specific uracil or 3,N4-ethenocytosine residue [2], significant role for double-stranded uracil-DNA glycosylase in mutation avoidance in non-dividing E. coli [3]. Uracil-DNA glycosylases are widespread enzymes that are found in all living organisms. Uracil-DNA glycosylase (EC 3.2.2.27) and EC 3.2.2.28 form a central part of the DNA-repair machinery since they initiate the DNA base-excision repair pathway by hydrolysing the N-glycosidic bond between uracil and the deoxyribose sugar thereby catalysing the removal of mis-incorporated uracil from DNA.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Barrett, T.E., Scharer, O.D., Savva, R., Brown, T., Jiricny, J., Verdine, G.L. and Pearl, L.H. Crystal structure of a thwarted mismatch glycosylase DNA repair complex. EMBO J. 18 (1999) 6599-6609. [PMID: 10581234]

2. Sung, J.S. and Mosbaugh, D.W. Escherichia coli double-strand uracil-DNA glycosylase: involvement in uracil-mediated DNA base excision repair and stimulation of activity by endonuclease IV. Biochemistry 39 (2000) 10224-10235. [PMID: 10956012]

3. Mokkapati, S.K., Fernandez de Henestrosa, A.R. and Bhagwat, A.S. Escherichia coli DNA glycosylase Mug: a growth-regulated enzyme required for mutation avoidance in stationary-phase cells. Mol. Microbiol. 41 (2001) 1101-1111. [PMID: 11555290]

[EC 3.2.2.28 created 2009]

EC 3.2.2.29

Accepted name: thymine-DNA glycosylase

Reaction: Hydrolyzes mismatched double-stranded DNA and polynucleotides, releasing free thymine

Other name(s): mismatch-specific thymine-DNA glycosylase; mismatch-specific thymine-DNA N-glycosylase; hTDG; hsTDG; TDG; thymine DNA glycosylase; G/T glycosylase; uracil/thymine DNA glycosylase; T:G mismatch-specific thymidine-DNA glycosylase; G:T mismatch-specific thymine DNA-glycosylase

Systematic name: thymine-DNA deoxyribohydrolase (thymine-releasing)

Comments: Thymine-DNA glycosylase is part of the DNA-repair machinery. Thymine removal is fastest when it is from a G/T mismatch with a 5'-flanking C/G pair. The glycosylase removes uracil from G/U, C/U, and T/U base pairs faster than it removes thymine from G/T [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Waters, T.R. and Swann, P.F. Thymine-DNA glycosylase and G to A transition mutations at CpG sites. Mutat Res 462 (2000) 137-147. [PMID: 10767625]

2. Neddermann, P. and Jiricny, J. The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. J. Biol. Chem. 268 (1993) 21218-21224. [PMID: 8407958]

3. Waters, T.R. and Swann, P.F. Kinetics of the action of thymine DNA glycosylase. J. Biol. Chem. 273 (1998) 20007-20014. [PMID: 9685338]

[EC 3.2.2.29 created 2009]

EC 3.2.2.30

Accepted name: aminodeoxyfutalosine nucleosidase

Reaction: 6-amino-6-deoxyfutalosine + H2O = dehypoxanthine futalosine + adenine

For diagram of reaction click here.

Glossary: 6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
dehypoxanthine futalosine = 3-{3-[(2R,3S,4R)-3,4,5-trihydroxytetrahydrofuran-2-yl]propanoyl}benzoate

Other name(s): AFL nucleosidase; aminofutalosine nucleosidase; methylthioadenosine nucleosidase; MqnB

Systematic name: 6-amino-6-deoxyfutalosine ribohydrolase

Comments: The enzyme, found in several bacterial species, catalyses a step in a modified futalosine pathway for menaquinone biosynthesis. While the enzyme from some organisms also has the activity of EC 3.2.2.9, adenosylhomocysteine nucleosidase, the enzyme from Chlamydia trachomatis is specific for 6-amino-6-deoxyfutalosine [7].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670-1673. [PMID: 18801996]

2. Li, X., Apel, D., Gaynor, E.C. and Tanner, M.E. 5'-methylthioadenosine nucleosidase is implicated in playing a key role in a modified futalosine pathway for menaquinone biosynthesis in Campylobacter jejuni. J. Biol. Chem. 286 (2011) 19392-19398. [PMID: 21489995]

3. Arakawa, C., Kuratsu, M., Furihata, K., Hiratsuka, T., Itoh, N., Seto, H. and Dairi, T. Diversity of the early step of the futalosine pathway. Antimicrob. Agents Chemother. 55 (2011) 913-916. [PMID: 21098241]

4. Wang, S., Haapalainen, A.M., Yan, F., Du, Q., Tyler, P.C., Evans, G.B., Rinaldo-Matthis, A., Brown, R.L., Norris, G.E., Almo, S.C. and Schramm, V.L. A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori. Biochemistry 51 (2012) 6892-6894. [PMID: 22891633]

5. Mishra, V. and Ronning, D.R. Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5'-alkylthio binding subsite. Biochemistry 51 (2012) 9763-9772. [PMID: 23148563]

6. Kim, R.Q., Offen, W.A., Davies, G.J. and Stubbs, K.A. Structural enzymology of Helicobacter pylori methylthioadenosine nucleosidase in the futalosine pathway. Acta Crystallogr. D Biol. Crystallogr. 70 (2014) 177-185. [PMID: 24419390]

7. Barta, M.L., Thomas, K., Yuan, H., Lovell, S., Battaile, K.P., Schramm, V.L. and Hefty, P.S. Structural and biochemical characterization of Chlamydia trachomatis hypothetical protein CT263 supports that menaquinone synthesis occurs through the futalosine pathway. J. Biol. Chem. 289 (2014) 32214-32229. [PMID: 25253688]

[EC 3.2.2.30 created 2014]

EC 3.2.2.31

Accepted name: adenine glycosylase

Reaction: Hydrolyses free adenine bases from 7,8-dihydro-8-oxoguanine:adenine mismatched double-stranded DNA, leaving an apurinic site.

Other name(s): mutY (gene name); A/G-specific adenine glycosylase

Systematic name: adenine-DNA deoxyribohydrolase (adenine-releasing)

Comments: The enzyme serves as a mismatch repair enzyme that works to correct 7,8-dihydro-8-oxoguanine:adenine mispairs that arise in DNA when error-prone synthesis occurs past 7,8-dihydro-8-oxoguanine (GO) lesions in DNA. The enzyme excises the adenine of the mispair, producing an apurinic site sensitive to AP endonuclease activity. After removing the undamaged adenine the enzyme remains bound to the site to prevent EC 3.2.2.23 (MutM) from removing the GO lesion, which could lead to a double strand break. In vitro the enzyme is also active with adenine:guanine, adenine:cytosine, and adenine:7,8-dihydro-8-oxoadenine (AO) mispairs, removing the adenine in all cases.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Au, K.G., Clark, S., Miller, J.H. and Modrich, P. Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs. Proc. Natl. Acad. Sci. USA 86 (1989) 8877-8881. [PMID: 2682664]

2. Michaels, M.L., Tchou, J., Grollman, A.P. and Miller, J.H. A repair system for 8-oxo-7,8-dihydrodeoxyguanine. Biochemistry 31 (1992) 10964-10968. [PMID: 1445834]

[EC 3.2.2.31 created 2018]


EC 3.2.3 Hydrolysing S-Glycosyl Compounds (discontinued)

[EC 3.2.3.1 Transferred entry: now EC 3.2.1.147 thioglucosidase (EC 3.2.3.1 created 1972, deleted 2001)]


Continued with EC 3.3.1 to EC 3.3.2
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