Methionyl-tRNA synthetase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P00959 (SYM_ECOLI)

Last modified June 16, 2009. Version 119. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Methionyl-tRNA synthetase
    EC=6.1.1.10
Alternative name(s):
    Methionine--tRNA ligase
      Short name=MetRS

Gene names

Name:	metG
Ordered Locus Names:	b2114, JW2101

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	677 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. HAMAP MF_00098
Catalytic activity	ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met). HAMAP MF_00098
Cofactor	Binds 1 zinc ion per subunit. HAMAP MF_00098
Subunit structure	Homodimer. HAMAP MF_00098
Subcellular location	Cytoplasm. HAMAP MF_00098
Sequence similarities	Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily. Contains 1 tRNA-binding domain.

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Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Metal-binding Nucleotide-binding RNA-binding Zinc tRNA-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	methionyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP methionine-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
rplB	P60422	1	EBI-909268,EBI-543515

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed HAMAP MF_00098

Chain

2 – 677

676

Methionyl-tRNA synthetase HAMAP MF_00098

PRO_0000139129

Regions

Domain

575 – 677

103

tRNA-binding

Motif

15 – 25

"HIGH" region HAMAP MF_00098

Motif

333 – 337

"KMSKS" region HAMAP MF_00098

Sites

Metal binding

146

Zinc HAMAP MF_00098

Metal binding

149

Zinc HAMAP MF_00098

Metal binding

159

Zinc HAMAP MF_00098

Metal binding

162

Zinc HAMAP MF_00098

Binding site

336

ATP HAMAP MF_00098

Experimental info

Mutagenesis

336

K → Q, A, E or R: Loss of activity. Ref.15

Secondary structure

677

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P00959-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 363F3324AFD3202C
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FASTA

677

76,255

        10         20         30         40         50         60 
MTQVAKKILV TCALPYANGS IHLGHMLEHI QADVWVRYQR MRGHEVNFIC ADDAHGTPIM 

        70         80         90        100        110        120 
LKAQQLGITP EQMIGEMSQE HQTDFAGFNI SYDNYHSTHS EENRQLSELI YSRLKENGFI 

       130        140        150        160        170        180 
KNRTISQLYD PEKGMFLPDR FVKGTCPKCK SPDQYGDNCE VCGATYSPTE LIEPKSVVSG 

       190        200        210        220        230        240 
ATPVMRDSEH FFFDLPSFSE MLQAWTRSGA LQEQVANKMQ EWFESGLQQW DISRDAPYFG 

       250        260        270        280        290        300 
FEIPNAPGKY FYVWLDAPIG YMGSFKNLCD KRGDSVSFDE YWKKDSTAEL YHFIGKDIVY 

       310        320        330        340        350        360 
FHSLFWPAML EGSNFRKPSN LFVHGYVTVN GAKMSKSRGT FIKASTWLNH FDADSLRYYY 

       370        380        390        400        410        420 
TAKLSSRIDD IDLNLEDFVQ RVNADIVNKV VNLASRNAGF INKRFDGVLA SELADPQLYK 

       430        440        450        460        470        480 
TFTDAAEVIG EAWESREFGK AVREIMALAD LANRYVDEQA PWVVAKQEGR DADLQAICSM 

       490        500        510        520        530        540 
GINLFRVLMT YLKPVLPKLT ERAEAFLNTE LTWDGIQQPL LGHKVNPFKA LYNRIDMRQV 

       550        560        570        580        590        600 
EALVEASKEE VKAAAAPVTG PLADDPIQET ITFDDFAKVD LRVALIENAE FVEGSDKLLR 

       610        620        630        640        650        660 
LTLDLGGEKR NVFSGIRSAY PDPQALIGRH TIMVANLAPR KMRFGISEGM VMAAGPGGKD 

       670 
IFLLSPDAGA KPGHQVK

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and primary structure of the Escherichia coli methionyl-tRNA synthetase gene." Dardel F., Fayat G., Blanquet S. J. Bacteriol. 160:1115-1122(1984) [PubMed: 6094501] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Transcription and regulation of expression of the Escherichia coli methionyl-tRNA synthetase gene." Dardel F., Panvert M., Fayat G. Mol. Gen. Genet. 223:121-133(1990) [PubMed: 2259334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Automated multiplex sequencing of the E.coli genome." Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / BHB2600.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Methionyl-tRNA synthetase from Escherichia coli. Primary structure of the active crystallised tryptic fragment." Barker D.G., Ebel J.-P., Jakes R., Bruton C.J. Eur. J. Biochem. 127:449-457(1982) [PubMed: 6756915] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-566, PARTIAL PROTEIN SEQUENCE.
[7]	"Crystal structure of Escherichia coli methionyl-tRNA synthetase at 2.5-A resolution." Zelwer C., Risler J.-L., Brunie S. J. Mol. Biol. 155:63-81(1982) [PubMed: 7042987] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[8]	"Crystallographic study at 2.5-A resolution of the interaction of methionyl-tRNA synthetase from Escherichia coli with ATP." Brunie S., Zelwer C., Risler J.-L. J. Mol. Biol. 216:411-424(1990) [PubMed: 2254937] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[9]	"Crystal structure of Escherichia coli methionyl-tRNA synthetase highlights species-specific features." Mechulam Y., Schmitt E., Maveyraud L., Zelwer C., Nureki O., Yokoyama S., Konno M., Blanquet S. J. Mol. Biol. 294:1287-1297(1999) [PubMed: 10600385] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.03 ANGSTROMS) OF 1-553.
[10]	"How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding." Serre L., Verdon G., Choinowski T., Hervouet N., Risler J.-L., Zelwer C. J. Mol. Biol. 306:863-876(2001) [PubMed: 11243794] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 1-552 IN COMPLEX WITH L-METHIONINE.
[11]	"Methionyl-tRNA synthetase zinc binding domain. Three-dimensional structure and homology with rubredoxin and gag retroviral proteins." Fourmy D., Dardel F., Blanquet S. J. Mol. Biol. 231:1078-1089(1993) [PubMed: 8515466] [Abstract] Cited for: STRUCTURE BY NMR OF 139-164.
[12]	"Mapping of the active site of Escherichia coli methionyl-tRNA synthetase: identification of amino acid residues labeled by periodate-oxidized tRNA(fMet) molecules having modified lengths at the 3'-acceptor end." Hountondji C., Schmitter J.-M., Beauvallet C., Blanquet S. Biochemistry 29:8190-8198(1990) [PubMed: 1702021] [Abstract] Cited for: ACTIVE SITE MAPPING.
[13]	"Methionyl-tRNA synthetase from E. coli -- a review." Meinnel T., Mechulam Y., Dardel F., Schmitter J.-M., Hountondji C., Brunie S., Dessen P., Fayat G., Blanquet S. Biochimie 72:625-632(1990) [PubMed: 2126467] [Abstract] Cited for: REVIEW.
[14]	"Identification of residues involved in the binding of methionine by Escherichia coli methionyl-tRNA synthetase." Fourmy D., Mechulam Y., Brunie S., Blanquet S., Fayat G. FEBS Lett. 292:259-263(1991) [PubMed: 1959615] [Abstract] Cited for: MUTAGENESIS.
[15]	"Mapping of the zinc binding domain of Escherichia coli methionyl-tRNA synthetase." Fourmy D., Meinnel T., Mechulam Y., Blanquet S. J. Mol. Biol. 231:1068-1077(1993) [PubMed: 8515465] [Abstract] Cited for: MUTAGENESIS OF ZINC LIGANDS.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

K02671 Genomic DNA. Translation: AAA24161.1.
X55791 Genomic DNA. Translation: CAA39315.1.
U00007 Genomic DNA. Translation: AAA60526.1. Different initiation.
U00096 Genomic DNA. Translation: AAC75175.1.
AP009048 Genomic DNA. Translation: BAE76592.1.

PIR

SYECMT. S14427.

RefSeq

AP_002712.1.
NP_416617.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F4L	X-ray	1.85	A	1-551	[»]
1MEA	NMR	-	A	139-164	[»]
1MED	NMR	-	A	139-164	[»]
1P7P	X-ray	1.80	A	2-551	[»]
1PFU	X-ray	1.91	A	2-551	[»]
1PFV	X-ray	1.70	A	2-551	[»]
1PFW	X-ray	1.78	A	2-551	[»]
1PFY	X-ray	1.93	A	2-551	[»]
1PG0	X-ray	1.90	A	2-551	[»]
1PG2	X-ray	1.75	A	2-551	[»]
1QQT	X-ray	2.03	A	2-552	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P00959. 3 interactions.

2-D gel databases

SWISS-2DPAGE

P00959.

ECO2DBASE

F072.0. 6TH EDITION.
G072.0. 6TH EDITION.

Genome annotation databases

GeneID

946643.

GenomeReviews

Gene locus JW2101 in contig AP009048_GR.
Gene locus b2114 in contig U00096_GR.

KEGG

ecj:JW2101.
eco:b2114.

Organism-specific databases

EchoBASE

EB0581.

EcoGene

EG10586. metG.

CMR

Search...

Phylogenomic databases

HOGENOM

P00959.

OMA

P00959. SAYQPEQ.

Enzyme and pathway databases

BioCyc

EcoCyc:METG-MON.
MetaCyc:METG-MON.

BRENDA

6.1.1.10. 246.

Family and domain databases

HAMAP

MF_00098.
[Tree]

InterPro

IPR015413. aa-tRNA-synt_I.
IPR001412. aa-tRNA-synth_I_CS.
IPR002304. Met-tRNA-synth_Ia.
IPR004495. Met-tRNA-synth_Ia_bsu_C.
IPR012340. NA-bd_OB-fold.
IPR014729. Rossmann-like_a/b/a_fold.
IPR014758. tRNA-synt_met_N.
IPR002547. tRNA_bd.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
G3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.

Pfam

PF09334. tRNA-synt_1g. 1 hit.
PF01588. tRNA_bind. 1 hit.
[Graphical view]

PRINTS

PR01041. TRNASYNTHMET.

TIGRFAMs

TIGR00398. metG. 1 hit.
TIGR00399. metG_C_term. 1 hit.

PROSITE

PS00178. AA_TRNA_LIGASE_I. 1 hit.
PS50886. TRBD. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

SYM_ECOLI

Accession

Primary (citable) accession number: P00959
Secondary accession number(s): Q2MAW4

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 119 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2-D gel databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents