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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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MetaCyc Enzyme: tRNA (cytidine/uridine-2'-O)-ribose methyltransferase

Gene: trmL Accession Numbers: EG11888 (MetaCyc), b3606, ECK3596

Synonyms: yibK

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of tRNA (cytidine/uridine-2'-O)-ribose methyltransferase = [TrmL]2
         tRNA (cytidine/uridine-2'-O)-ribose methyltransferase = TrmL

Summary:
TrmL is the methyltransferase responsible for 2'-O-methylation of the wobble nucleotide 34 (cytidine or uridine) ribose in both tRNALeu isoacceptors [BenitezPaez10]. TrmL showed no methyltransferase activity with certain synthetic tRNA substrates [Purta06]; the enzyme requires the presence of the ms2i6 modification at the A37 nucleotide for activity [BenitezPaez10, Liu13c]. In addition, the A35 nucleotide functions as an identity element for substrate recognition by TrmL [BenitezPaez10].

TrmL belongs to the SPOUT superfamily of methyltransferases [Koonin93, Anantharaman02] and is a dimer in solution [Purta06, BenitezPaez10]. Crystal structures of the enzyme have been solved, allowing the identification of the SAM co-substrate binding site and the predicted active site. Residues predicted to be involved in tRNA binding were investigated by site-directed mutagenesis [Liu13c].

A trmL mutant does not have a growth defect in rich medium. However, experiments using several cycles of competitive growth revealed a defect compared to wild type, which is possibly related to recovery from stationary phase [BenitezPaez10].

TrmL: "tRNA methyltransferase L" [BenitezPaez10]

Locations: cytosol

Map Position: [3,779,238 -> 3,779,711]

Molecular Weight of Polypeptide: 17.726 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011790 , EchoBASE:EB1834 , EcoGene:EG11888 , EcoliWiki:b3606 , Mint:MINT-1308881 , ModBase:P0AGJ7 , OU-Microarray:b3606 , PortEco:yibK , Pride:P0AGJ7 , Protein Model Portal:P0AGJ7 , RefSeq:NP_418063 , RegulonDB:EG11888 , SMR:P0AGJ7 , String:511145.b3606 , Swiss-Model:P0AGJ7 , UniProt:P0AGJ7

Relationship Links: InterPro:IN-FAMILY:IPR001537 , InterPro:IN-FAMILY:IPR016914 , PDB:Structure:4JAK , PDB:Structure:4JAL , Pfam:IN-FAMILY:PF00588

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0002131 - wobble position cytosine ribose methylation Inferred from experiment [BenitezPaez10]
GO:0002132 - wobble position uridine ribose methylation Inferred from experiment [BenitezPaez10]
GO:0001510 - RNA methylation Inferred by computational analysis [GOA01]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0030488 - tRNA methylation Inferred by computational analysis [GOA06]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0042803 - protein homodimerization activity Inferred from experiment [BenitezPaez10]
GO:0052665 - tRNA (uracil-2'-O-)-methyltransferase activity Inferred from experiment [BenitezPaez10]
GO:0052666 - tRNA (cytosine-2'-O-)-methyltransferase activity Inferred from experiment [BenitezPaez10]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0008173 - RNA methyltransferase activity Inferred by computational analysis [GOA01]
GO:0008175 - tRNA methyltransferase activity Inferred by computational analysis [GOA06]
GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity Inferred by computational analysis [GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Credits:
Created in EcoCyc 07-Sep-2006 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: tRNA (5-carboxymethylaminomethyluridine)-ribose methyltransferase (tRNA (cytidine/uridine-2'-O)-ribose methyltransferase)

EC Number: 2.1.1.207

a 5-carboxymethylaminomethyluridine34 in tRNALeu + S-adenosyl-L-methionine <=> a 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu + 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

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
a 5-carboxymethylaminomethyluridine34 in tRNALeu
1.17
0.0098
[Liu13c]


Enzymatic reaction of: tRNA (cytidine-2'-O)-ribose methyltransferase (tRNA (cytidine/uridine-2'-O)-ribose methyltransferase)

EC Number: 2.1.1.207

a cytidine34 in tRNA + S-adenosyl-L-methionine <=> a 2'-O-methylcytidine34 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 direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

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

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
a cytidine34 in tRNA
3.39
0.0073
[Liu13c]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 78
[UniProt10b]
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 100
[UniProt10b]
UniProt: S-adenosyl-L-methionine; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 122
[UniProt10b]
UniProt: S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 130
[UniProt10b]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;

History:
10/20/97 Gene b3606 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11888.


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

BenitezPaez10: Benitez-Paez A, Villarroya M, Douthwaite S, Gabaldon T, Armengod ME (2010). "YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors." RNA 16(11);2131-43. PMID: 20855540

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Liu13c: Liu RJ, Zhou M, Fang ZP, Wang M, Zhou XL, Wang ED (2013). "The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL." Nucleic Acids Res 41(16);7828-42. PMID: 23804755

Purta06: Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM (2006). "The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase." BMC Mol Biol 7;23. PMID: 16848900

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-12 released on 2010-12-01 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."


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 Sat Dec 20, 2014, BIOCYC13A.