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] |
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[EC 2.1.1.386 created 2022] |
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EC
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2.7.7.20
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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] |
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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
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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] |
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[EC 2.7.8.42 created 2015] |
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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] |
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[EC 2.8.1.4 created 1984, modified 2017] |
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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].
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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] |
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[EC 3.5.4.37 created 2013] |
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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
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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] |
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[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] |
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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] |
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[EC 6.1.1.6 created 1961] |
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EC
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6.1.1.8
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Deleted entry: | D-alanine-sRNA synthetase |
[EC 6.1.1.8 created 1961, deleted 1965] |
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