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MetaCyc Enzyme: tRNA (Gm18) 2'-O-methyltransferase

Gene: trmH Accession Numbers: EG10967 (MetaCyc), b3651, ECK3641

Synonyms: spoU

Species: Escherichia coli K-12 substr. MG1655

Summary:
TrmH is the methyltransferase responsible for 2'-O-methylation of ribose at position G18 in certain tRNAs [Persson97]. Unlike Type I enzymes (e.g. from Thermus thermophilus) that can modify all tRNA species, the E. coli enzyme is a Type II enzyme that only modifies a subset of tRNAs. The catalytic domain of TrmH is responsible for substrate selectivity [Ochi13].

TrmH belongs to the SPOUT superfamily of methyltransferases [Anantharaman02] and was identified early as a member of a protein family predicted to include rRNA methylases [Koonin93].

[Persson97] reported no growth defect of a trmH in LB or MOPS-glucose medium, while [Urbonavicius02] found a lower growth rate in rich-MOPS medium compared to wild type. The ΔspoU3 insertion-deletion allele of trmH causes phenotypes due to polar effects on recG gene expression [Kalman92]. A trmH trmA truB triple mutant shows a defect in the tRNA modifications Gm18, m5U54, and Ψ55 as well as translation defects, heat sensitivity, and a growth defect [Urbonavicius02].

Interestingly, tRNATyr lacking the Gm18 modification elicits release of interferon-α in human peripheral blood, while the modified tRNA does not [Jockel12, Gehrig12].

TrmH: "tRNA methylation" [Persson97]

Review: [El12]

Citations: [Kinghorn02, Gustafsson96]

Locations: cytosol

Map Position: [3,822,538 -> 3,823,227]

Molecular Weight of Polypeptide: 25.343 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011937 , CGSC:33877 , DIP:DIP-35977N , EchoBASE:EB0960 , EcoGene:EG10967 , EcoliWiki:b3651 , ModBase:P0AGJ2 , OU-Microarray:b3651 , PortEco:trmH , PR:PRO_000024115 , Pride:P0AGJ2 , Protein Model Portal:P0AGJ2 , RefSeq:NP_418108 , RegulonDB:EG10967 , SMR:P0AGJ2 , String:511145.b3651 , Swiss-Model:P0AGJ2 , UniProt:P0AGJ2

Relationship Links: InterPro:IN-FAMILY:IPR001537 , InterPro:IN-FAMILY:IPR022724 , Pfam:IN-FAMILY:PF00588 , Pfam:IN-FAMILY:PF12105

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0002938 - tRNA guanine ribose methylation Inferred from experiment [Persson97]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01a]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0030488 - tRNA methylation Author statement [Persson97]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0009020 - tRNA (guanosine-2'-O-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Ochi13, Persson97]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0008173 - RNA methyltransferase activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: tRNA (Gm18) 2'-O-methyltransferase

Synonyms: tRNA guanosine 2'-methyltransferase

EC Number: 2.1.1.34

a guanosine18 in tRNA + S-adenosyl-L-methionine <=> a 2'-O-methylguanosine18 in tRNA + S-adenosyl-L-homocysteine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 119
[UniProt10a]
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 139
[UniProt10a]
UniProt: S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 148
[UniProt10a]
UniProt: S-adenosyl-L-methionine; via amide nitrogen; Non-Experimental Qualifier: by similarity;

History:
10/20/97 Gene b3651 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10967; confirmed by SwissProt match.


References

Anantharaman02: Anantharaman V, Koonin EV, Aravind L (2002). "SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases." J Mol Microbiol Biotechnol 4(1);71-5. PMID: 11763972

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

El12: El Yacoubi B, Bailly M, de Crecy-Lagard V (2012). "Biosynthesis and function of posttranscriptional modifications of transfer RNAs." Annu Rev Genet 46;69-95. PMID: 22905870

Gehrig12: Gehrig S, Eberle ME, Botschen F, Rimbach K, Eberle F, Eigenbrod T, Kaiser S, Holmes WM, Erdmann VA, Sprinzl M, Bec G, Keith G, Dalpke AH, Helm M (2012). "Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity." J Exp Med 209(2);225-33. PMID: 22312113

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Gustafsson96: Gustafsson C, Reid R, Greene PJ, Santi DV (1996). "Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes." Nucleic Acids Res 24(19);3756-62. PMID: 8871555

Jockel12: Jockel S, Nees G, Sommer R, Zhao Y, Cherkasov D, Hori H, Ehm G, Schnare M, Nain M, Kaufmann A, Bauer S (2012). "The 2'-O-methylation status of a single guanosine controls transfer RNA-mediated Toll-like receptor 7 activation or inhibition." J Exp Med 209(2);235-41. PMID: 22312111

Kalman92: Kalman M, Murphy H, Cashel M (1992). "The nucleotide sequence of recG, the distal spo operon gene in Escherichia coli K-12." Gene 110(1);95-9. PMID: 1544582

Kinghorn02: Kinghorn SM, O'Byrne CP, Booth IR, Stansfield I (2002). "Physiological analysis of the role of truB in Escherichia coli: a role for tRNA modification in extreme temperature resistance." Microbiology 148(Pt 11);3511-20. PMID: 12427942

Koonin93: Koonin EV, Rudd KE (1993). "SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases." Nucleic Acids Res 21(23);5519. PMID: 8265370

Ochi13: Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H (2013). "The Catalytic Domain of Topological Knot tRNA Methyltransferase (TrmH) Discriminates between Substrate tRNA and Nonsubstrate tRNA via an Induced-fit Process." J Biol Chem 288(35);25562-74. PMID: 23867454

Persson97: Persson BC, Jager G, Gustafsson C (1997). "The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity." Nucleic Acids Res 25(20);4093-7. PMID: 9321663

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Urbonavicius02: Urbonavicius J, Durand JM, Bjork GR (2002). "Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri." J Bacteriol 184(19);5348-57. PMID: 12218021


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Tue Nov 25, 2014, biocyc13.