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Escherichia coli K-12 substr. MG1655 Enzyme: tRNA (cytidine/uridine-2'-O)-ribose methyltransferase



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

Synonyms: yibK

Regulation Summary Diagram: ?

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] (81.45 centisomes)
Length: 474 bp / 157 aa

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

In Paralogous Gene Group: 435 (4 members)

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

Essentiality data for trmL knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Created 07-Sep-2006 by Keseler I , SRI International
Last-Curated ? 09-Jul-2013 by Keseler I , 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.

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.

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;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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(1);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 EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Dec 18, 2014, biocyc12.