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Escherichia coli K-12 substr. MG1655 Enzyme: tRNA m7G46 methyltransferase



Gene: trmI Accession Numbers: EG11779 (EcoCyc), b2960, ECK2955

Synonyms: trmB, yggH

Regulation Summary Diagram: ?

Summary:
tRNA m7G46 methyltransferase (TrmI) catalyzes methylation of N(7) of the G46 position in the variable loop of tRNAs [De03].

Based on a homology model of TrmI (TrmB), potential catalytic residues have been mutagenized; kinetic analysis of the mutant enzymes showed a significant reduction in methyltransferase activity for most mutants [Purta05]. Crystal structures of TrmI alone and in complexes with SAM and SAH have been solved, showing that the enzyme adopts a modified Rossmann fold [Liu08a, Zhou09].

A trmI mutant lacks m7G in tRNAs [De03]. In an earlier study, a trmB mutant lacking m7G was isolated and mapped to 6' on the E. coli chromosome [Marinus75]. The relationship between trmB and trmI is unclear.

Locations: cytosol

Map Position: [3,100,155 <- 3,100,874] (66.82 centisomes)
Length: 720 bp / 239 aa

Molecular Weight of Polypeptide: 27.307 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009714 , DIP:DIP-36015N , EchoBASE:EB1727 , EcoGene:EG11779 , EcoliWiki:b2960 , ModBase:P0A8I5 , OU-Microarray:b2960 , PortEco:trmI , Pride:P0A8I5 , Protein Model Portal:P0A8I5 , RefSeq:NP_417435 , RegulonDB:EG11779 , SMR:P0A8I5 , String:511145.b2960 , UniProt:P0A8I5

Relationship Links: InterPro:IN-FAMILY:IPR003358 , PDB:Structure:3DXX , PDB:Structure:3DXY , PDB:Structure:3DXZ , Pfam:IN-FAMILY:PF02390 , Prosite:IN-FAMILY:PS51625

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0030488 - tRNA methylation Inferred from experiment [De03]
GO:0036265 - RNA (guanine-N7)-methylation Inferred from experiment [De03]
GO:0006400 - tRNA modification Inferred by computational analysis [GOA06, GOA01]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0008176 - tRNA (guanine-N7-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, De03]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for trmI 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:
Last-Curated ? 05-Apr-2013 by Keseler I , SRI International


Enzymatic reaction of: tRNA m7G46 methyltransferase

Synonyms: tRNA (guanine-N7-)-methyltransferase, S-adenosyl-L-methionine:tRNA (guanine-N7-)-methyltransferase, transfer ribonucleate guanine 7-methyltransferase, 7-methylguanine transfer ribonucleate methylase, tRNA guanine 7-methyltransferase, N7-methylguanine methylase

EC Number: 2.1.1.33

guanine46 in tRNA + S-adenosyl-L-methionine <=> N7-methylguanine46 in tRNA + S-adenosyl-L-homocysteine

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.

Summary:
The enzyme was initially purified from E. coli MRE 600 [Aschhoff76].

Citations: [De03]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
S-adenosyl-L-methionine
16.0
[HURWITZ64, BRENDA14]
S-adenosyl-L-methionine
6.0
3.6
[Purta05]

pH(opt): 7.5 [BRENDA14, HURWITZ64]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 26
[Purta05, UniProt11a]
Alternate sequence: R → A; UniProt: Reduces catalytic activity over 10- fold.
Amino-Acid-Sites-That-Bind 69
[UniProt10a]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 94
[UniProt10a]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 121
[UniProt10a]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Active-Site 144
[UniProt14]
UniProt: Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 144
[Purta05, UniProt11a]
Alternate sequence: D → A; UniProt: Loss of activity.
Amino-Acid-Sites-That-Bind 144
[UniProt10a]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 148
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 150
[Purta05, UniProt11a]
Alternate sequence: R → A; UniProt: Reduces catalytic activity about 3- fold.
Protein-Segment 150 -> 155
[UniProt10a]
UniProt: Interaction with RNA; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 151
[Purta05, UniProt11a]
Alternate sequence: H → A; UniProt: Reduces catalytic activity over 10- fold.
Mutagenesis-Variant 152
[Purta05, UniProt11a]
Alternate sequence: N → A; UniProt: No effect.
Mutagenesis-Variant 154
[Purta05, UniProt11a]
Alternate sequence: R → A; UniProt: Loss of activity.
Mutagenesis-Variant 155
[Purta05, UniProt11a]
Alternate sequence: R → A; UniProt: Loss of activity.
Mutagenesis-Variant 180
[Purta05, UniProt11a]
Alternate sequence: D → A; UniProt: Reduces catalytic activity over 10- fold.
Amino-Acid-Sites-That-Bind 180
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 217
[Purta05, UniProt11a]
Alternate sequence: T → A; UniProt: Reduces catalytic activity over 10- fold.
Protein-Segment 217 -> 220
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 220
[Purta05, UniProt11a]
Alternate sequence: E → A; UniProt: Reduces catalytic activity 10-fold.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b2960 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11779; confirmed by SwissProt match.


References

Aschhoff76: Aschhoff HJ, Elten H, Arnold HH, Mahal G, Kersten W, Kersten H (1976). "7-Methylguanine specific tRNA-methyltransferase from Escherichia coli." Nucleic Acids Res 3(11);3109-22. PMID: 794833

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

De03: De Bie LG, Roovers M, Oudjama Y, Wattiez R, Tricot C, Stalon V, Droogmans L, Bujnicki JM (2003). "The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase." J Bacteriol 185(10);3238-43. PMID: 12730187

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

HURWITZ64: HURWITZ J, GOLD M, ANDERS M (1964). "THE ENZYMATIC METHYLATION OF RIBONUCLEIC ACID AND DEOXYRIBONUCLEIC ACID. IV. THE PROPERTIES OF THE SOLUBLE RIBONUCLEIC ACID-METHYLATING ENZYMES." J Biol Chem 239;3474-82. PMID: 14245405

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

Liu08a: Liu Q, Yang W, Zhou H, Gao Y, Zhang X, Teng M, Niu L (2008). "Crystallization and preliminary crystallographic analysis of tRNA (m(7)G46) methyltransferase from Escherichia coli." Acta Crystallogr Sect F Struct Biol Cryst Commun 64(Pt 8);743-5. PMID: 18678947

Marinus75: Marinus MG, Morris NR, Soll D, Kwong TC (1975). "Isolation and partial characterization of three Escherichia coli mutants with altered transfer ribonucleic acid methylases." J Bacteriol 122(1);257-65. PMID: 1091626

Purta05: Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM (2005). "Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis." Proteins 59(3);482-8. PMID: 15789416

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

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

Zhou09: Zhou H, Liu Q, Yang W, Gao Y, Teng M, Niu L (2009). "Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion." Proteins 76(2);512-5. PMID: 19373903


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 Sun Dec 21, 2014, BIOCYC13A.