Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

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, Liu13a]. 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 [Liu13a].

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 [UniProtGOA11]
GO:0030488 - tRNA methylation Inferred by computational analysis [GOA06]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11]
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 [UniProtGOA11, 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 [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, 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
[Liu13a]


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
[Liu13a]


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

Liu13a: 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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms 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 Wed Nov 26, 2014, biocyc13.