Type-2 seryl-tRNA synthetase - Methanococcoides burtonii (strain DSM 6242)

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Reviewed, UniProtKB/Swiss-Prot Q12TN5 (SYS2_METBU)

Last modified February 9, 2010. Version 29. 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:	Mbur_2337

Organism

Methanococcoides burtonii (strain DSM 6242) [Complete proteome] [HAMAP]

Taxonomic identifier

259564 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanomicrobia › Methanosarcinales › Methanosarcinaceae › Methanococcoides

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Protein attributes

Sequence length	502 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

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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) By similarity. HAMAP MF_01278
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. HAMAP MF_01278
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 By similarity. HAMAP MF_01278
Subcellular location	Cytoplasm By similarity HAMAP MF_01278.
Domain	Consists of two distinct domains, a catalytic core and a N-terminal extension that is presumably involved in tRNA binding By similarity. HAMAP MF_01278
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family. Type-2 seryl-tRNA synthetase subfamily.

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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 – 502

502

Type-2 seryl-tRNA synthetase HAMAP MF_01278

PRO_0000286168

Regions

Nucleotide binding

336 – 338

ATP By similarity

Nucleotide binding

347 – 348

ATP By similarity

Region

353 – 355

Serine binding By similarity

Sites

Metal binding

306

Zinc; catalytic By similarity

Metal binding

355

Zinc; catalytic By similarity

Metal binding

461

Zinc; catalytic By similarity

Binding site

304

Serine; via carbonyl oxygen By similarity

Binding site

336

Serine By similarity

Binding site

400

Serine By similarity

Binding site

432

ATP By similarity

Binding site

435

Serine By similarity

Binding site

468

ATP By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q12TN5-1 [UniParc].

Last modified August 22, 2006. Version 1.
Checksum: E3DA16D5AC8FDF58
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FASTA

502

57,388

        10         20         30         40         50         60 
MELKFNLKGA FKTSTDPTGA KEVIAQYFDE ANNTILKKGA PEGQGAKITQ WDIVDGSIEL 

        70         80         90        100        110        120 
TIESGRYVRA HDAIMRLKKP LAAKLGKEFR IGIRGVDVKK FTISMPAEGE IGNMNIPHVS 

       130        140        150        160        170        180 
NISKVEGGLI LELNVGESEL ERRIPDRILT LMEEKVRAKD YGGKAEHWQI LWESDKKEHT 

       190        200        210        220        230        240 
FAGDPTQEMM KHGWIKRGAS RGQWIHGPQS TKMFRTFEKI VYDELLEPLG YREMIFPKLV 

       250        260        270        280        290        300 
PWEVWQKSGH AKGVYPEIYY VCPPKTRDPA YWEEVSDHYK VTHEVPTELI KSKIGDPIGG 

       310        320        330        340        350        360 
LCYAQCPPFW MYLQGETIPT DEFPIKVFDK SGTSHRYESG GIHGIERVDE FHRVEIVWLG 

       370        380        390        400        410        420 
TKEQVIETAR KLHERYMHIF NEILDLEWRK AWVTPWFMAQ EGLTGLSEQG EAGTTDYEAP 

       430        440        450        460        470        480 
LPYRGDDGEW LEFQNVSING NKYPSGFNVK SQTGEELWSG CSGVGLERWA SAFFAQKGLD 

       490        500 
PENWPEEFRK RVGEVPKGIR FL

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References

[1]

"Complete sequence of Methanococcoides burtonii DSM 6242."
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Kadner K., Aerts A., Dehal P., Pitluck S., Martinez M., Schmutz J., Larimer F., Land M.

Richardson P.
Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000300 Genomic DNA. Translation: ABE53191.1.
RefSeq	YP_566941.1.
3D structure databases
SMR	Q12TN5. Positions 1-502.
ModBase	Search...
Protein-protein interaction databases
STRING	Q12TN5.
Genome annotation databases
GeneID	3998918.
GenomeReviews	Gene locus Mbur_2337 in contig CP000300_GR.
KEGG	mbu:Mbur_2337.
NMPDR	fig\|259564.8.peg.2241.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	arNOG04799.
HOGENOM	HBG542255.
OMA	PAQCEPF.
Enzyme and pathway databases
BioCyc	MBUR259564:MBUR_2337-MONOMER.
Family and domain databases
HAMAP	MF_01278. Ser_tRNA_synth_type2. [Tree]
InterPro	IPR002314. aa-tRNA-synt_IIb_cons-dom. [Graphical view]
Pfam	PF00587. tRNA-synt_2b. 1 hit. [Graphical view]
PROSITE	PS50862. AA_TRNA_LIGASE_II. False negative. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

SYS2_METBU

Accession

Primary (citable) accession number: Q12TN5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 2007
Last sequence update:	August 22, 2006
Last modified:	February 9, 2010
This is version 29 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

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

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents