The Enzyme Database

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EC 2.1.1.386     
Accepted name: small RNA 2′-O-methyltransferase
Reaction: S-adenosyl-L-methionine + an [sRNA]-3′-end ribonucleotide = S-adenosyl-L-homocysteine + an [sRNA]-3′-end 2′-O-methylated ribonucleotide
Glossary: sRNA = small RNA
Other name(s): HENMT1 (gene name); HEN1 (gene name)
Systematic name: S-adenosyl-L-methionine:[sRNA]-3′-end ribonucleotide 2′-O-methyltransferase
Comments: The enzyme adds a 2′-O-methyl group to the ribose of the last nucleotide in several types of small RNAs (sRNAs), protecting the 3′-end of sRNAs from uridylation activity and subsequent degradation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Park, W., Li, J., Song, R., Messing, J. and Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12 (2002) 1484–1495. [DOI] [PMID: 12225663]
2.  Yu, B., Yang, Z., Li, J., Minakhina, S., Yang, M., Padgett, R.W., Steward, R. and Chen, X. Methylation as a crucial step in plant microRNA biogenesis. Science 307 (2005) 932–935. [DOI] [PMID: 15705854]
3.  Kirino, Y. and Mourelatos, Z. 2′-O-methyl modification in mouse piRNAs and its methylase. Nucleic Acids Symp Ser (Oxf) (2007) 417–418. [DOI] [PMID: 18029764]
4.  Huang, Y., Ji, L., Huang, Q., Vassylyev, D.G., Chen, X. and Ma, J.B. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461 (2009) 823–827. [DOI] [PMID: 19812675]
5.  Peng, L., Zhang, F., Shang, R., Wang, X., Chen, J., Chou, J.J., Ma, J., Wu, L. and Huang, Y. Identification of substrates of the small RNA methyltransferase Hen1 in mouse spermatogonial stem cells and analysis of its methyl-transfer domain. J. Biol. Chem. 293 (2018) 9981–9994. [DOI] [PMID: 29703750]
[EC 2.1.1.386 created 2022]
 
 
EC 2.7.7.20      
Deleted entry: sRNA nucleotidyl transferase. This entry was identical with EC 2.7.7.25, tRNA adenylyltransferase
[EC 2.7.7.20 created 1965, deleted 1972]
 
 
EC 2.7.8.42     
Accepted name: Kdo2-lipid A phosphoethanolamine 7′′-transferase
Reaction: (1) diacylphosphatidylethanolamine + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A = diacylglycerol + 7-O-[2-aminoethoxy(hydroxy)phosphoryl]-α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A
(2) diacylphosphatidylethanolamine + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid IVA = diacylglycerol + 7-O-[2-aminoethoxy(hydroxy)phosphoryl]-α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid IVA
Glossary: lipid A = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid IVA = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
Other name(s): eptB (gene name)
Systematic name: diacylphosphatidylethanolamine:α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid-A 7′′-phosphoethanolaminetransferase
Comments: The enzyme has been characterized from the bacterium Escherichia coli. It is activated by Ca2+ ions and is silenced by the sRNA MgrR.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kanipes, M.I., Lin, S., Cotter, R.J. and Raetz, C.R. Ca2+-induced phosphoethanolamine transfer to the outer 3-deoxy-D-manno-octulosonic acid moiety of Escherichia coli lipopolysaccharide. A novel membrane enzyme dependent upon phosphatidylethanolamine. J. Biol. Chem. 276 (2001) 1156–1163. [DOI] [PMID: 11042192]
2.  Reynolds, C.M., Kalb, S.R., Cotter, R.J. and Raetz, C.R. A phosphoethanolamine transferase specific for the outer 3-deoxy-D-manno-octulosonic acid residue of Escherichia coli lipopolysaccharide. Identification of the eptB gene and Ca2+ hypersensitivity of an eptB deletion mutant. J. Biol. Chem. 280 (2005) 21202–21211. [DOI] [PMID: 15795227]
3.  Moon, K., Six, D.A., Lee, H.J., Raetz, C.R. and Gottesman, S. Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification. Mol. Microbiol. 89 (2013) 52–64. [DOI] [PMID: 23659637]
[EC 2.7.8.42 created 2015]
 
 
EC 2.8.1.4     
Accepted name: tRNA uracil 4-sulfurtransferase
Reaction: ATP + [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + uracil in tRNA + 2 reduced ferredoxin [iron-sulfur] cluster = AMP + diphosphate + 4-thiouracil in tRNA + [ThiI sulfur-carrier protein]-L-cysteine + 2 oxidized ferredoxin [iron-sulfur] cluster
Other name(s): thiI (gene name); transfer ribonucleate sulfurtransferase (ambiguous); RNA sulfurtransferase (ambiguous); ribonucleate sulfurtransferase (ambiguous); transfer RNA sulfurtransferase (ambiguous); transfer RNA thiolase (ambiguous); L-cysteine:tRNA sulfurtransferase (incorrect); tRNA sulfurtransferase (ambiguous)
Systematic name: [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine:uracil in tRNA sulfurtransferase
Comments: The enzyme, found in bacteria and archaea, is activated by EC 2.8.1.7, cysteine desulfurase, which transfers a sulfur atom to an internal L-cysteine residue, forming a cysteine persulfide. The activated enzyme then transfers the sulfur to a uridine in a tRNA chain in a reaction that requires ATP. The enzyme from the bacterium Escherichia coli forms 4-thiouridine only at position 8 of tRNA. The enzyme also participates in the biosynthesis of the thiazole moiety of thiamine, but different domains are involved in the two processes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9055-57-6
References:
1.  Abrell, J.W., Kaufman, E.E. and Lipsett, M.N. The biosynthesis of 4-thiouridylate. Separation and purification of two enzymes in the transfer ribonucleic acid-sulfurtransferase system. J. Biol. Chem. 246 (1971) 294–301. [PMID: 5541999]
2.  Hayward, R.S. and Weiss, S.B. RNA thiolase: the enzymatic transfer of sulfur from cysteine to sRNA in Escherichia coli extracts. Proc. Natl. Acad. Sci. USA 55 (1966) 1161–1168. [DOI] [PMID: 5334200]
3.  Lipsett, M.N. and Peterkofsky, A. Enzymatic thiolation of E. coli sRNA. Proc. Natl. Acad. Sci. USA 55 (1966) 1169–1174. [DOI] [PMID: 5334201]
4.  Wong, T., Weiss, S.B., Eliceiri, G.L. and Bryant, J. Ribonucleic acid sulfurtransferase from Bacillus subtilis W168. Sulfuration with β-mercaptopyruvate and properties of the enzyme system. Biochemistry 9 (1970) 2376–2386. [PMID: 4987417]
5.  Kambampati, R. and Lauhon, C.T. Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. J. Biol. Chem. 275 (2000) 10727–10730. [DOI] [PMID: 10753862]
6.  Mueller, E.G., Palenchar, P.M. and Buck, C.J. The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA. J. Biol. Chem. 276 (2001) 33588–33595. [DOI] [PMID: 11443125]
7.  Lauhon, C.T., Erwin, W.M. and Ton, G.N. Substrate specificity for 4-thiouridine modification in Escherichia coli. J. Biol. Chem. 279 (2004) 23022–23029. [DOI] [PMID: 15037613]
8.  Neumann, P., Lakomek, K., Naumann, P.T., Erwin, W.M., Lauhon, C.T. and Ficner, R. Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. Nucleic Acids Res. 42 (2014) 6673–6685. [DOI] [PMID: 24705700]
9.  Liu, Y., Vinyard, D.J., Reesbeck, M.E., Suzuki, T., Manakongtreecheep, K., Holland, P.L., Brudvig, G.W. and Soll, D. A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc. Natl. Acad. Sci. USA 113 (2016) 12703–12708. [DOI] [PMID: 27791189]
[EC 2.8.1.4 created 1984, modified 2017]
 
 
EC 3.5.4.37     
Accepted name: double-stranded RNA adenine deaminase
Reaction: adenine in double-stranded RNA + H2O = hypoxanthine in double-stranded RNA + NH3
Other name(s): ADAR; double-stranded RNA adenosine deaminase; dsRAD; dsRNA adenosine deaminase; DRADA1; double-stranded RNA-specific adenosine deaminase
Systematic name: double-stranded RNA adenine aminohydrolase
Comments: This eukaryotic enzyme is involved in RNA editing. It destabilizes double-stranded RNA through conversion of adenosine to inosine. Inositol hexakisphosphate is required for activity [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Hough, R.F. and Bass, B.L. Purification of the Xenopus laevis double-stranded RNA adenosine deaminase. J. Biol. Chem. 269 (1994) 9933–9939. [PMID: 8144588]
2.  O'Connell, M.A., Gerber, A. and Keegan, L.P. Purification of native and recombinant double-stranded RNA-specific adenosine deaminases. Methods 15 (1998) 51–62. [DOI] [PMID: 9614652]
3.  Wong, S.K., Sato, S. and Lazinski, D.W. Substrate recognition by ADAR1 and ADAR2. RNA 7 (2001) 846–858. [PMID: 11421361]
4.  Macbeth, M.R., Schubert, H.L., Vandemark, A.P., Lingam, A.T., Hill, C.P. and Bass, B.L. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science 309 (2005) 1534–1539. [DOI] [PMID: 16141067]
[EC 3.5.4.37 created 2013]
 
 
EC 4.6.1.19     
Accepted name: ribonuclease T2
Reaction: RNA + H2O = an [RNA fragment]-3′-nucleoside-3′-phosphate + a 5′-hydroxy-ribonucleotide-3′-[RNA fragment] (overall reaction)
(1a) RNA = an [RNA fragment]-3′-nucleoside-2′,3′-cyclophosphate + a 5′-hydroxy-ribonucleotide-3′-[RNA fragment]
(1b) an [RNA fragment]-3′-nucleoside-2′,3′-cyclophosphate + H2O = an [RNA fragment]-3′-nucleoside-3′-phosphate
Other name(s): ribonuclease II; base-non-specific ribonuclease; nonbase-specific RNase; RNase (non-base specific); non-base specific ribonuclease; nonspecific RNase; RNase Ms; RNase M; RNase II; Escherichia coli ribonuclease II; ribonucleate nucleotido-2′-transferase (cyclizing); acid ribonuclease; RNAase CL; Escherichia coli ribonuclease I′ ribonuclease PP2; ribonuclease N2; ribonuclease M; acid RNase; ribonnuclease (non-base specific); ribonuclease (non-base specific); RNase T2; ribonuclease PP3; ribonucleate 3′-oligonucleotide hydrolase; ribonuclease U4
Systematic name: [RNA] 5′-hydroxy-ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′- nucleoside-2′,3′-cyclophosphate-forming and hydrolysing)
Comments: A widely distributed family of related enzymes found in protozoans, plants, bacteria, animals and viruses that cleave ssRNA 3′-phosphate group with little base specificity. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5′-hydroxy-phosphooligonucletides and 3′-phosphooligonucleotides ending with a 2′,3′-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses the cyclic products in a second reaction that takes place only when all the susceptible 3′,5′-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5′-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3′-nucleotides.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37278-25-4
References:
1.  Garcia-Segura, J.M., Orozco, M.M., Fominaya, J.M. and Gavilanes, J.G. Purification, molecular and enzymic characterization of an acid RNase from the insect Ceratitis capitata. Eur. J. Biochem. 158 (1986) 367–372. [DOI] [PMID: 3732273]
2.  Heppel, L.A. Pig liver nuclei ribonuclease. In: Cantoni, G.L. and Davies, D.R. (Ed.), Procedures in Nucleic Acid Research, Procedures in Nucleic Acid Research, New York, 1966, pp. 31–36.
3.  Reddi, K.K. and Mauser, L.J. Studies on the formation of tobacco mosaic virus ribonucleic acid. VI. Mode of degradation of host ribonucleic acid to ribonucleosides and their conversion to ribonucleoside 5′-phosphates. Proc. Natl. Acad. Sci. USA 53 (1965) 607–613. [PMID: 14338240]
4.  Uchida, I. and Egami, F. The specificity of ribonuclease T2. J. Biochem. (Tokyo) 61 (1967) 44–53. [PMID: 6048969]
5.  Irie, M. and Ohgi, K. Ribonuclease T2. Methods Enzymol. 341 (2001) 42–55. [PMID: 11582795]
6.  Luhtala, N. and Parker, R. T2 Family ribonucleases: ancient enzymes with diverse roles. Trends Biochem. Sci. 35 (2010) 253–259. [PMID: 20189811]
[EC 4.6.1.19 created 1972 as EC 3.1.4.23, transferred 1978 to EC 3.1.27.1, modified 1981, transferred 2018 to EC 4.6.1.19]
 
 
EC 6.1.1.6     
Accepted name: lysine—tRNA ligase
Reaction: ATP + L-lysine + tRNALys = AMP + diphosphate + L-lysyl-tRNALys
Other name(s): lysyl-tRNA synthetase; lysyl-transfer ribonucleate synthetase; lysyl-transfer RNA synthetase; L-lysine-transfer RNA ligase; lysine-tRNA synthetase; lysine translase
Systematic name: L-lysine:tRNALys ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9031-26-9
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. [PMID: 13792726]
2.  Chiumecka, V., von Tigerstrom, M., D'Obrenan, P. and Smith, C.J. Purification and properties of lysyl transfer ribonucleic acid synthetase from bakers' yeast. J. Biol. Chem. 244 (1969) 5481–5488. [PMID: 4310598]
3.  Lagerkvist, U., Rymo, L., Lindqvist, O. and Andersson, E. Some properties of crystals of lysine transfer ribonucleic acid ligase from yeast. J. Biol. Chem. 247 (1972) 3897–3899. [PMID: 4555953]
4.  Stern, R. and Mehler, A.H. Lysyl-sRNA synthetase from Escherichia coli. Biochem. Z. 342 (1965) 400–409. [PMID: 4284804]
[EC 6.1.1.6 created 1961]
 
 
EC 6.1.1.8      
Deleted entry:  D-alanine-sRNA synthetase
[EC 6.1.1.8 created 1961, deleted 1965]
 
 


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