Type-2 seryl-tRNA synthetase - Methanocaldococcus jannaschii

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Reviewed, UniProtKB/Swiss-Prot Q58477 (SYS2_METJA)

Last modified November 3, 2009. Version 60. History...

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

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Names and origin

Protein names

Recommended name:
    Type-2 seryl-tRNA synthetase
    EC=6.1.1.11
Alternative name(s):
    Seryl-tRNA(Ser/Sec) synthetase
    Serine--tRNA ligase
      Short name=SerRS

Gene names

Name:	serS
Ordered Locus Names:	MJ1077

Organism

Methanocaldococcus jannaschii (Methanococcus jannaschii) [Complete proteome] [HAMAP]

Taxonomic identifier

2190 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

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Protein attributes

Sequence length	521 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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.2
Catalytic activity	ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser). HAMAP MF_01278 ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec). HAMAP MF_01278
Cofactor	Binds 1 Zn²⁺ ion per subunit. This ion is coordinated with 2 cysteines, 1 glutamate and a water molecule that dissociates from the zinc ion to allow the coordination of the amino group of the serine substrate, which is essential for catalysis By similarity.
Pathway	Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. HAMAP MF_01278
Subunit structure	Homodimer. Ref.2
Subcellular location	Cytoplasm By similarity.
Domain	Consists of two distinct domains, a catalytic core and a N-terminal extension that is presumably involved in tRNA binding By similarity.
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family. Type-2 seryl-tRNA synthetase subfamily.
Biophysicochemical properties	Temperature dependence: Thermostable. Fully active at 80 degrees Celsius. HAMAP MF_01278

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Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	selenocysteine biosynthetic process Inferred from electronic annotation. Source: HAMAP seryl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP serine-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 521

521

Type-2 seryl-tRNA synthetase HAMAP MF_01278

PRO_0000122174

Regions

Nucleotide binding

347 – 349

ATP By similarity

Nucleotide binding

358 – 359

ATP By similarity

Region

364 – 366

Serine binding By similarity

Sites

Metal binding

318

Zinc; catalytic By similarity

Metal binding

366

Zinc; catalytic By similarity

Metal binding

473

Zinc; catalytic By similarity

Binding site

316

Serine; via carbonyl oxygen By similarity

Binding site

347

Serine By similarity

Binding site

480

ATP By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q58477-1 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: E8D40DB16915B4FE
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FASTA

521

60,632

        10         20         30         40         50         60 
MKLTFDLDGK IIFSKELSEE AKNAVEEVLK NADSIFLKGV PKGKENEASK IKSYEFEGNI 

        70         80         90        100        110        120 
LKLKIASGTY TRAHEGLIRL RKPLAEKLGR NFRIGVRGIE IDNYVITIET DEDKAKKLEG 

       130        140        150        160        170        180 
IKVPECEAKV EGNKIILTFK DIGESELKRN IIDRAIKFVK TELEKEEEDL TFKVCKIPPG 

       190        200        210        220        230        240 
TIVSEYKAKR KITFDKDPTD VAEKLGWVKK FPGRGQWFYT PPITALFRAL EELIVEEVVK 

       250        260        270        280        290        300 
KIGFQECLFP KLIPLEIMYK MRYLEGLPEG MYYVCPPKRE PELFKEFVNE MMIKKEIPIE 

       310        320        330        340        350        360 
KLKNLLRDPG YVLAPAQCEP FYQFFEGEVI DVDKPIMFFD RSGWTYRWEG GGARGLDRVN 

       370        380        390        400        410        420 
EFLRVECVWI GSPEFVEETR DKTLKYAEKL AEKLDLEYWV EVGDDPFYLE GRKKEDRGIE 

       430        440        450        460        470        480 
FPDVPKYEMR LWLPHIKDER KGVAVTSANV HGTHFVEGFR IKDYKGRRVW TGCTGYGITR 

       490        500        510        520 
WVVGYLAQYG FNFDDWHPII KKKIKKLPEV PQLITWPKKD E

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. Venter J.C. Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"The unusual methanogenic seryl-tRNA synthetase recognizes tRNASer species from all three kingdoms of life." Bilokapic S., Korencic D., Soell D., Weygand-Durasevic I. Eur. J. Biochem. 271:694-702(2004) [PubMed: 14764085] [Abstract] Cited for: FUNCTION, SUBUNIT, TEMPERATURE DEPENDENCE. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

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Cross-references

Sequence databases
	L77117 Genomic DNA. Translation: AAB99075.1.
PIR	D64434.
RefSeq	NP_248070.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	1451973.
GenomeReviews	Gene locus MJ1077 in contig L77117_GR.
KEGG	mja:MJ1077.
NMPDR	fig\|243232.1.peg.1107.
TIGR	MJ1077.
Phylogenomic databases
HOGENOM	Q58477.
OMA	PAQCEPF.
Enzyme and pathway databases
BioCyc	MJAN243232:MJ_1077-MON.
BRENDA	6.1.1.11. 256362.
Family and domain databases
HAMAP	MF_01278. [Tree]
InterPro	IPR002314. aa-tRNA-synt_IIb_cons-reg. IPR004503. Ser-tRNA-synth_IIa_arc. [Graphical view]
Pfam	PF00587. tRNA-synt_2b. 1 hit. [Graphical view]
TIGRFAMs	TIGR00415. serS_MJ. 1 hit.
PROSITE	PS50862. AA_TRNA_LIGASE_II. False negative. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

SYS2_METJA

Accession

Primary (citable) accession number: Q58477

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	November 1, 1996
Last modified:	November 3, 2009
This is version 60 of the entry and version 1 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

Methanococcus jannaschii

Methanococcus jannaschii: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents