Serine--tRNA ligase - Escherichia coli (strain K12)

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P0A8L1 (SYS_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 77. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Serine--tRNA ligase
EC=6.1.1.11

Alternative name(s):
Seryl-tRNA synthetase
Short name=SerRS
Seryl-tRNA(Ser/Sec) synthetase

Gene names

Name:	serS
Ordered Locus Names:	b0893, JW0876

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	430 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). Ref.6 Ref.9 Ref.10
Catalytic activity	ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser). HAMAP-Rule MF_00176 ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec). HAMAP-Rule MF_00176
Pathway	Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. HAMAP-Rule MF_00176
Subunit structure	Homodimer. The tRNA molecule binds across the dimer. Ref.8 Ref.10
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_00176.
Domain	Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. Ref.8 Ref.9
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=64 µM for serine Ref.9 Ref.10 K_M=0.068 µM for ATP

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	selenocysteine biosynthetic process Inferred from direct assay PubMed 1939093. Source: EcoCyc selenocysteinyl-tRNA(Sec) biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway seryl-tRNA aminoacylation Inferred from direct assay Ref.10. Source: UniProtKB
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from direct assay PubMed 17889423. Source: EcoCyc serine-tRNA ligase activity Inferred from direct assay Ref.10. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-548422,EBI-548422

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 430

430

Serine--tRNA ligase HAMAP-Rule MF_00176

PRO_0000122044

Regions

Nucleotide binding

268 – 270

ATP By similarity

Nucleotide binding

355 – 358

ATP By similarity

Region

237 – 239

Serine binding By similarity

Sites

Binding site

291

Serine By similarity

Binding site

391

Serine By similarity

Experimental info

Mutagenesis

355

E → Q: Loss of serine activation activity. Ref.10

Sequences

Sequence

Length

Mass (Da)

Tools

P0A8L1 [UniParc].

Last modified June 7, 2005. Version 1.
Checksum: 87675745A512A626
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FASTA

430

48,414

        10         20         30         40         50         60 
MLDPNLLRNE PDAVAEKLAR RGFKLDVDKL GALEERRKVL QVKTENLQAE RNSRSKSIGQ 

        70         80         90        100        110        120 
AKARGEDIEP LRLEVNKLGE ELDAAKAELD ALQAEIRDIA LTIPNLPADE VPVGKDENDN 

       130        140        150        160        170        180 
VEVSRWGTPR EFDFEVRDHV TLGEMHSGLD FAAAVKLTGS RFVVMKGQIA RMHRALSQFM 

       190        200        210        220        230        240 
LDLHTEQHGY SENYVPYLVN QDTLYGTGQL PKFAGDLFHT RPLEEEADTS NYALIPTAEV 

       250        260        270        280        290        300 
PLTNLVRGEI IDEDDLPIKM TAHTPCFRSE AGSYGRDTRG LIRMHQFDKV EMVQIVRPED 

       310        320        330        340        350        360 
SMAALEEMTG HAEKVLQLLG LPYRKIILCT GDMGFGACKT YDLEVWIPAQ NTYREISSCS 

       370        380        390        400        410        420 
NVWDFQARRM QARCRSKSDK KTRLVHTLNG SGLAVGRTLV AVMENYQQAD GRIEVPEVLR 

       430 
PYMNGLEYIG

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of the gene for Escherichia coli seryl-tRNA synthetase." Haertlein M., Madern D., Leberman R. Nucleic Acids Res. 15:1005-1017(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Nucleotide sequence of the dmsABC operon encoding the anaerobic dimethylsulphoxide reductase of Escherichia coli." Bilous P.T., Cole S.T., Anderson W.F., Weiner J.H. Mol. Microbiol. 2:785-795(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 251-430.
[6]	"Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine." Leinfelder W., Zehelein E., Mandrand-Berthelot M.A., Boeck A. Nature 331:723-725(1988) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A SERYL-TRNA(SEC) SYNTHETASE.
[7]	"Escherichia coli seryl-tRNA synthetase: the structure of a class 2 aminoacyl-tRNA synthetase." Leberman R., Haertlein M., Cusack S. Biochim. Biophys. Acta 1089:287-298(1991) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[8]	"Crystallization of the seryl-tRNA synthetase:tRNA(Ser) complex of Escherichia coli." Price S., Cusack S., Borel F., Berthet-Colominas C., Leberman R. FEBS Lett. 324:167-170(1993) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, DOMAIN, CRYSTALLIZATION.
[9]	"Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity." Borel F., Vincent C., Leberman R., Haertlein M. Nucleic Acids Res. 22:2963-2969(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, KINETIC PARAMETERS, DOMAIN.
[10]	"Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation." Vincent C., Borel F., Willison J.C., Leberman R., Haertlein M. Nucleic Acids Res. 23:1113-1118(1995) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, KINETIC PARAMETERS, MUTAGENESIS OF GLU-355, SUBUNIT, REACTION MECHANISM.
[11]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[12]	"A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A." Cusack S., Berthet-Colominas C., Haertlein M., Nassar N., Leberman R. Nature 347:249-255(1990) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X05017 Genomic DNA. Translation: CAA28673.1. U00096 Genomic DNA. Translation: AAC73979.1. AP009048 Genomic DNA. Translation: BAA35625.1. J03412 Genomic DNA. Translation: AAA83842.1.
PIR	YSEC. A26400.
RefSeq	NP_415413.1. NC_000913.2. YP_489165.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0A8L1.
SMR	P0A8L1. Positions 1-423.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-35989N.
IntAct	P0A8L1. 16 interactions.
MINT	MINT-1230011.
STRING	511145.b0893.
2D gel databases
SWISS-2DPAGE	P0A8L1.
Proteomic databases
PaxDb	P0A8L1.
PRIDE	P0A8L1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC73979; AAC73979; b0893. BAA35625; BAA35625; BAA35625.
GeneID	12932491. 945506.
KEGG	ecj:Y75_p0865. eco:b0893.
PATRIC	32116997. VBIEscCol129921_0923.
Organism-specific databases
EchoBASE	EB0940.
EcoGene	EG10947. serS.
Phylogenomic databases
eggNOG	COG0172.
HOGENOM	HOG000035938.
KO	K01875.
OMA	EESWEWH.
ProtClustDB	PRK05431.
Enzyme and pathway databases
BioCyc	EcoCyc:SERS-MONOMER. ECOL316407:JW0876-MONOMER. MetaCyc:SERS-MONOMER.
UniPathway	UPA00906; UER00895.
Gene expression databases
Genevestigator	P0A8L1.
Family and domain databases
Gene3D	1.10.287.40. 1 hit.
HAMAP	MF_00176. Ser_tRNA_synth_type1.
InterPro	IPR002314. aa-tRNA-synt_IIb_cons-dom. IPR006195. aa-tRNA-synth_II. IPR002317. Ser-tRNA-ligase_type_1. IPR015866. Ser-tRNA-synth_1_N. IPR010978. tRNA-bd_arm. [Graphical view]
PANTHER	PTHR11778. PTHR11778. 1 hit.
Pfam	PF02403. Seryl_tRNA_N. 1 hit. PF00587. tRNA-synt_2b. 1 hit. [Graphical view]
PIRSF	PIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
PRINTS	PR00981. TRNASYNTHSER.
SUPFAM	SSF46589. tRNA_binding_arm. 1 hit.
TIGRFAMs	TIGR00414. serS. 1 hit.
PROSITE	PS50862. AA_TRNA_LIGASE_II. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

SYS_ECOLI

Accession

Primary (citable) accession number: P0A8L1
Secondary accession number(s): P09156

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

Escherichia coli

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

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

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents