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Escherichia coli K-12 substr. MG1655 Enzyme: methionyl-tRNA synthetase



Gene: metG Accession Numbers: EG10586 (EcoCyc), b2114, ECK2107

Synonyms: MetRS

Regulation Summary Diagram: ?

Subunit composition of methionyl-tRNA synthetase = [MetG]2
         methionyl-tRNA synthetase = MetG

Summary:
Methionyl-tRNA synthetase (MetRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. MetRS belongs to the Class I aminoacyl tRNA synthetases; apart from sequence motifs whithin the active site, the different enzymes show little similarity in their primary amino acid sequences [Eriani90, Landes95].

The metG gene has been cloned by complementation of the metG83 mutation [Dardel84]. Mutagenesis of the metG gene has been used to study the domain structure of the enzyme [Mellot89].

Several X-ray crystal structures have been determined [Zelwer82, Brunie90, Mechulam99, Serre01]. Methionine and methionyl adenylate analogues have been used to study conformational changes during catalysis [Crepin03].

Citations: [Meinnel90]

Locations: cytosol, membrane

Map Position: [2,192,322 -> 2,194,355] (47.25 centisomes)
Length: 2034 bp / 677 aa

Molecular Weight of Polypeptide: 76.255 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006991 , CGSC:510 , DIP:DIP-10194N , EchoBASE:EB0581 , EcoGene:EG10586 , EcoliWiki:b2114 , ModBase:P00959 , OU-Microarray:b2114 , PortEco:metG , PR:PRO_000023213 , Pride:P00959 , Protein Model Portal:P00959 , RefSeq:NP_416617 , RegulonDB:EG10586 , SMR:P00959 , String:511145.b2114 , Swiss-Model:P00959 , UniProt:P00959

Relationship Links: InterPro:IN-FAMILY:IPR001412 , InterPro:IN-FAMILY:IPR002547 , InterPro:IN-FAMILY:IPR004495 , InterPro:IN-FAMILY:IPR009080 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR014758 , InterPro:IN-FAMILY:IPR015413 , InterPro:IN-FAMILY:IPR023458 , PDB:Structure:1F4L , PDB:Structure:1MEA , PDB:Structure:1MED , PDB:Structure:1P7P , PDB:Structure:1PFU , PDB:Structure:1PFV , PDB:Structure:1PFW , PDB:Structure:1PFY , PDB:Structure:1PG0 , PDB:Structure:1PG2 , PDB:Structure:1QQT , PDB:Structure:3H97 , PDB:Structure:3H99 , PDB:Structure:3H9B , PDB:Structure:3H9C , Pfam:IN-FAMILY:PF01588 , Pfam:IN-FAMILY:PF09334 , Prints:IN-FAMILY:PR01041 , Prosite:IN-FAMILY:PS00178 , Prosite:IN-FAMILY:PS50886

In Paralogous Gene Group: 7 (4 members) , 150 (2 members) , 378 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01a]
GO:0006431 - methionyl-tRNA aminoacylation Inferred by computational analysis [GOA06, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06]
GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004825 - methionine-tRNA ligase activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for metG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Enzymatic reaction of: methionyl-tRNA synthetase

EC Number: 6.1.1.10

tRNAmet + L-methionine + ATP + H+ <=> L-methionyl-tRNAmet + AMP + diphosphate

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.

In Pathways: tRNA charging

Cofactors or Prosthetic Groups: Zn2+ [Xu93, Landro93, Fourmy93, Fourmy93a]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-methionine
22.0
[Lawrence73, BRENDA14]
L-methionine
78.0
[Armstrong75, BRENDA14]
ATP
550.0
[Lawrence73, BRENDA14]
tRNAmet
3.9
1.0
[Casina11, BRENDA14]
tRNAmet
0.9
3.3
[Meinnel90, BRENDA14]
tRNAmet
1000.0
6.85
[Kim98, BRENDA14]
tRNAmet
4.4, 20.0
2.8, 42.0
[Crepin02, BRENDA14]

pH(opt): 8 [BRENDA14, Green09a]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt10]
UniProt: Removed;
Chain 2 -> 677
[UniProt09]
UniProt: Methionyl-tRNA synthetase;
Protein-Segment 15 -> 25
[UniProt10]
UniProt: "HIGH" region; Sequence Annotation Type: short sequence motif;
Metal-Binding-Site 146
[UniProt10]
UniProt: Zinc;
Metal-Binding-Site 149
[UniProt10]
UniProt: Zinc;
Metal-Binding-Site 159
[UniProt10]
UniProt: Zinc;
Metal-Binding-Site 162
[UniProt10]
UniProt: Zinc;
Protein-Segment 333 -> 337
[UniProt10]
UniProt: "KMSKS" region; Sequence Annotation Type: short sequence motif;
Mutagenesis-Variant 336
[Fourmy93a, UniProt11]
Alternate sequence: K → R; UniProt: Loss of activity.
Alternate sequence: K → E; UniProt: Loss of activity.
Alternate sequence: K → A; UniProt: Loss of activity.
Alternate sequence: K → Q; UniProt: Loss of activity.
Amino-Acid-Sites-That-Bind 336
[UniProt10]
UniProt: ATP;
Conserved-Region 575 -> 677
[UniProt09]
UniProt: tRNA-binding;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2114 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10586; confirmed by SwissProt match.


References

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

Armstrong75: Armstrong JB, Fairfield JA (1975). "A new method for the isolation of methionyl transfer RNA synthetase mutants from Escherichia coli." Can J Microbiol 21(6);754-8. PMID: 1097064

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.

Brunie90: Brunie S, Zelwer C, Risler JL (1990). "Crystallographic study at 2.5 A resolution of the interaction of methionyl-tRNA synthetase from Escherichia coli with ATP." J Mol Biol 216(2);411-24. PMID: 2254937

Casina11: Casina VC, Lobashevsky AA, McKinney WE, Brown CL, Alexander RW (2011). "Role for a conserved structural motif in assembly of a class I aminoacyl-tRNA synthetase active site." Biochemistry 50(5);763-9. PMID: 21175197

Crepin02: Crepin T, Schmitt E, Blanquet S, Mechulam Y (2002). "Structure and function of the C-terminal domain of methionyl-tRNA synthetase." Biochemistry 41(43);13003-11. PMID: 12390027

Crepin03: Crepin T, Schmitt E, Mechulam Y, Sampson PB, Vaughan MD, Honek JF, Blanquet S (2003). "Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase." J Mol Biol 332(1);59-72. PMID: 12946347

Dardel84: Dardel F, Fayat G, Blanquet S (1984). "Molecular cloning and primary structure of the Escherichia coli methionyl-tRNA synthetase gene." J Bacteriol 160(3);1115-22. PMID: 6094501

Eriani90: Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs." Nature 347(6289);203-6. PMID: 2203971

Fourmy93: Fourmy D, Dardel F, Blanquet S (1993). "Methionyl-tRNA synthetase zinc binding domain. Three-dimensional structure and homology with rubredoxin and gag retroviral proteins." J Mol Biol 231(4);1078-89. PMID: 8515466

Fourmy93a: Fourmy D, Meinnel T, Mechulam Y, Blanquet S (1993). "Mapping of the zinc binding domain of Escherichia coli methionyl-tRNA synthetase." J Mol Biol 231(4);1068-77. PMID: 8515465

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."

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

Green09a: Green LS, Bullard JM, Ribble W, Dean F, Ayers DF, Ochsner UA, Janjic N, Jarvis TC (2009). "Inhibition of methionyl-tRNA synthetase by REP8839 and effects of resistance mutations on enzyme activity." Antimicrob Agents Chemother 53(1);86-94. PMID: 19015366

Kim98: Kim S, Jo YJ, Lee SH, Motegi H, Shiba K, Sassanfar M, Martinis SA (1998). "Biochemical and phylogenetic analyses of methionyl-tRNA synthetase isolated from a pathogenic microorganism, Mycobacterium tuberculosis." FEBS Lett 427(2);259-62. PMID: 9607323

Landes95: Landes C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL (1995). "A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases." Biochimie 77(3);194-203. PMID: 7647112

Landro93: Landro JA, Schimmel P (1993). "Metal-binding site in a class I tRNA synthetase localized to a cysteine cluster inserted into nucleotide-binding fold." Proc Natl Acad Sci U S A 90(6);2261-5. PMID: 8460131

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Lawrence73: Lawrence F (1973). "Effect of adenosine on methionyl-tRNA synthetase." Eur J Biochem 40(2);493-500. PMID: 4592651

Mechulam99: Mechulam Y, Schmitt E, Maveyraud L, Zelwer C, Nureki O, Yokoyama S, Konno M, Blanquet S (1999). "Crystal structure of Escherichia coli methionyl-tRNA synthetase highlights species-specific features." J Mol Biol 294(5);1287-97. PMID: 10600385

Meinnel90: Meinnel T, Mechulam Y, Dardel F, Schmitter JM, Hountondji C, Brunie S, Dessen P, Fayat G, Blanquet S (1990). "Methionyl-tRNA synthetase from E. coli--a review." Biochimie 72(8);625-32. PMID: 2126467

Mellot89: Mellot P, Mechulam Y, Le Corre D, Blanquet S, Fayat G (1989). "Identification of an amino acid region supporting specific methionyl-tRNA synthetase: tRNA recognition." J Mol Biol 208(3);429-43. PMID: 2477552

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Rosevear88: Rosevear PR (1988). "Purification and NMR studies of [methyl-13C]methionine-labeled truncated methionyl-tRNA synthetase." Biochemistry 27(20);7931-9. PMID: 3061464

Serre01: Serre L, Verdon G, Choinowski T, Hervouet N, Risler JL, Zelwer C (2001). "How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding." J Mol Biol 306(4);863-76. PMID: 11243794

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

Xu93: Xu B, Krudy GA, Rosevear PR (1993). "Identification of the metal ligands and characterization of a putative zinc finger in methionyl-tRNA synthetase." J Biol Chem 268(22);16259-64. PMID: 8344912

Zelwer82: Zelwer C, Risler JL, Brunie S (1982). "Crystal structure of Escherichia coli methionyl-tRNA synthetase at 2.5 A resolution." J Mol Biol 155(1);63-81. PMID: 7042987

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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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 Nov 27, 2014, biocyc13.