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P34945 (SYS_THET2) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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:TT_C0520
OrganismThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) [Complete proteome] [HAMAP]
Taxonomic identifier262724 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length421 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the attachment of serine to tRNA(Ser). Is also probably 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). HAMAP-Rule MF_00176

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. A single tRNA molecule binds across the dimer. Ref.2 Ref.4 Ref.5

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. HAMAP-Rule MF_00176

Sequence similarities

Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily.

Ontologies

Keywords
   Biological processProtein biosynthesis
   Cellular componentCytoplasm
   LigandATP-binding
Nucleotide-binding
   Molecular functionAminoacyl-tRNA synthetase
Ligase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processselenocysteine biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-HAMAP

selenocysteinyl-tRNA(Sec) biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

seryl-tRNA aminoacylation

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

serine-tRNA ligase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 421421Serine--tRNA ligase HAMAP-Rule MF_00176
PRO_0000122145

Regions

Nucleotide binding256 – 2583ATP HAMAP-Rule MF_00176
Nucleotide binding345 – 3484ATP HAMAP-Rule MF_00176
Region225 – 2273Serine binding HAMAP-Rule MF_00176

Sites

Binding site2721ATP; via amide nitrogen and carbonyl oxygen
Binding site2791Serine
Binding site3801Serine

Secondary structure

....................................................................... 421
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P34945 [UniParc].

Last modified May 24, 2004. Version 2.
Checksum: 5E89B0D131EFC209

FASTA42147,813
        10         20         30         40         50         60 
MVDLKRLRQE PEVFHRAIRE KGVALDLEAL LALDREVQEL KKRLQEVQTE RNQVAKRVPK 

        70         80         90        100        110        120 
APPEEKEALI ARGKALGEEA KRLEEALREK EARLEALLLQ VPLPPWPGAP VGGEEANREI 

       130        140        150        160        170        180 
KRVGGPPEFS FPPLDHVALM EKNGWWEPRI SQVSGSRSYA LKGDLALYEL ALLRFAMDFM 

       190        200        210        220        230        240 
ARRGFLPMTL PSYAREKAFL GTGHFPAYRD QVWAIAETDL YLTGTAEVVL NALHSGEILP 

       250        260        270        280        290        300 
YEALPLRYAG YAPAFRSEAG SFGKDVRGLM RVHQFHKVEQ YVLTEASLEA SDRAFQELLE 

       310        320        330        340        350        360 
NAEEILRLLE LPYRLVEVAT GDMGPGKWRQ VDIEVYLPSE GRYRETHSCS ALLDWQARRA 

       370        380        390        400        410        420 
NLRYRDPEGR VRYAYTLNNT ALATPRILAM LLENHQLQDG RVRVPQALIP YMGKEVLEPC 


G 

« Hide

References

« Hide 'large scale' references
[1]"The genome sequence of the extreme thermophile Thermus thermophilus."
Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T., Liesegang H., Johann A., Lienard T., Gohl O., Martinez-Arias R., Jacobi C., Starkuviene V., Schlenczeck S., Dencker S., Huber R., Klenk H.-P., Kramer W., Merkl R., Gottschalk G., Fritz H.-J.
Nat. Biotechnol. 22:547-553(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HB27 / ATCC BAA-163 / DSM 7039.
[2]"Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5-A resolution."
Fujinaga M., Berthet-Colominas C., Yaremchuk A.D., Tukalo M.A., Cusack S.
J. Mol. Biol. 234:222-233(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.
[3]"Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate."
Belrhali H., Yaremchuk A.D., Tukalo M.A., Larsen K., Berthet-Colominas C., Leberman R., Beijer B., Sproat B., Als-Nielsen J., Gruebel G., Legrand J.-F., Lehmann M., Cusack S.
Science 263:1432-1436(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE ANALOGS.
[4]"The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser)."
Biou V., Yaremchuk A.D., Tukalo M.A., Cusack S.
Science 263:1404-1410(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA(SER), SUBUNIT.
[5]"The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site."
Cusack S., Yaremchuk A.D., Tukalo M.A.
EMBO J. 15:2834-2842(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH TRNA(SER) AND SUBSTRATE ANALOG, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE017221 Genomic DNA. Translation: AAS80868.1.
RefSeqYP_004495.1. NC_005835.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1SERX-ray2.90A/B1-421[»]
1SESX-ray2.50A/B1-421[»]
1SETX-ray2.55A/B1-421[»]
1SRYX-ray2.50A/B1-421[»]
3ERRX-ray2.27A/B1-419[»]
DisProtDP00514.
ProteinModelPortalP34945.
SMRP34945. Positions 1-421.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING262724.TTC0520.

Chemistry

DrugBankDB00131. Adenosine monophosphate.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAS80868; AAS80868; TT_C0520.
GeneID2775083.
KEGGtth:TTC0520.
PATRIC23951447. VBITheThe54392_0520.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0172.
KOK01875.
OMAEQQIDLK.
OrthoDBEOG61KBH9.
ProtClustDBPRK05431.

Enzyme and pathway databases

BioCycTTHE262724:GCAT-532-MONOMER.
UniPathwayUPA00906; UER00895.

Family and domain databases

Gene3D1.10.287.40. 1 hit.
HAMAPMF_00176. Ser_tRNA_synth_type1.
InterProIPR002314. 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]
PANTHERPTHR11778. PTHR11778. 1 hit.
PfamPF02403. Seryl_tRNA_N. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
PIRSFPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
PRINTSPR00981. TRNASYNTHSER.
SUPFAMSSF46589. SSF46589. 1 hit.
TIGRFAMsTIGR00414. serS. 1 hit.
PROSITEPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP34945.

Entry information

Entry nameSYS_THET2
AccessionPrimary (citable) accession number: P34945
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: May 24, 2004
Last modified: February 19, 2014
This is version 107 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries