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Protein

Serine--tRNA ligase

Gene

serS

Organism
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).

Catalytic activityi

ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec).

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei272 – 2721ATP; via amide nitrogen and carbonyl oxygen
Binding sitei279 – 2791Serine
Binding sitei380 – 3801Serine

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi256 – 2583ATP
Nucleotide bindingi345 – 3484ATP

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. serine-tRNA ligase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. selenocysteine biosynthetic process Source: UniProtKB-HAMAP
  2. selenocysteinyl-tRNA(Sec) biosynthetic process Source: UniProtKB-UniPathway
  3. seryl-tRNA aminoacylation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciTTHE262724:GCAT-532-MONOMER.
BRENDAi6.1.1.11. 2305.
UniPathwayiUPA00906; UER00895.

Names & Taxonomyi

Protein namesi
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 namesi
Name:serS
Ordered Locus Names:TT_C0520
OrganismiThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Taxonomic identifieri262724 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000592 Componenti: Chromosome

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 421421Serine--tRNA ligasePRO_0000122145Add
BLAST

Interactioni

Subunit structurei

Homodimer. A single tRNA molecule binds across the dimer.3 Publications

Protein-protein interaction databases

STRINGi262724.TTC0520.

Structurei

Secondary structure

1
421
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 96Combined sources
Helixi11 – 2111Combined sources
Helixi27 – 5731Combined sources
Beta strandi58 – 614Combined sources
Helixi63 – 653Combined sources
Helixi94 – 985Combined sources
Beta strandi111 – 1133Combined sources
Helixi114 – 1163Combined sources
Beta strandi118 – 1247Combined sources
Helixi136 – 1438Combined sources
Helixi150 – 1545Combined sources
Helixi163 – 18220Combined sources
Beta strandi186 – 1894Combined sources
Beta strandi192 – 1954Combined sources
Helixi196 – 2027Combined sources
Turni205 – 2084Combined sources
Helixi209 – 2113Combined sources
Turni216 – 2194Combined sources
Beta strandi220 – 2223Combined sources
Helixi227 – 2326Combined sources
Turni233 – 2364Combined sources
Beta strandi238 – 2403Combined sources
Helixi241 – 2433Combined sources
Beta strandi245 – 25511Combined sources
Beta strandi268 – 2714Combined sources
Beta strandi273 – 28412Combined sources
Helixi288 – 30821Combined sources
Beta strandi313 – 3175Combined sources
Turni320 – 3223Combined sources
Beta strandi328 – 33710Combined sources
Helixi338 – 3403Combined sources
Beta strandi342 – 35312Combined sources
Helixi355 – 3606Combined sources
Beta strandi363 – 3653Combined sources
Beta strandi371 – 3733Combined sources
Beta strandi375 – 38410Combined sources
Helixi386 – 39510Combined sources
Helixi406 – 4083Combined sources
Helixi409 – 4124Combined sources
Beta strandi413 – 4175Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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/B94-419[»]
DisProtiDP00514.
ProteinModelPortaliP34945.
SMRiP34945. Positions 1-421.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP34945.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni225 – 2273Serine binding

Domaini

Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding.

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0172.
KOiK01875.
OMAiFADDMFR.
OrthoDBiEOG61KBH9.

Family and domain databases

Gene3Di1.10.287.40. 1 hit.
HAMAPiMF_00176. Ser_tRNA_synth_type1.
InterProiIPR002314. 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]
PANTHERiPTHR11778. PTHR11778. 1 hit.
PfamiPF02403. Seryl_tRNA_N. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
PIRSFiPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
PRINTSiPR00981. TRNASYNTHSER.
SUPFAMiSSF46589. SSF46589. 1 hit.
TIGRFAMsiTIGR00414. serS. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P34945-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVDLKRLRQE PEVFHRAIRE KGVALDLEAL LALDREVQEL KKRLQEVQTE
60 70 80 90 100
RNQVAKRVPK APPEEKEALI ARGKALGEEA KRLEEALREK EARLEALLLQ
110 120 130 140 150
VPLPPWPGAP VGGEEANREI KRVGGPPEFS FPPLDHVALM EKNGWWEPRI
160 170 180 190 200
SQVSGSRSYA LKGDLALYEL ALLRFAMDFM ARRGFLPMTL PSYAREKAFL
210 220 230 240 250
GTGHFPAYRD QVWAIAETDL YLTGTAEVVL NALHSGEILP YEALPLRYAG
260 270 280 290 300
YAPAFRSEAG SFGKDVRGLM RVHQFHKVEQ YVLTEASLEA SDRAFQELLE
310 320 330 340 350
NAEEILRLLE LPYRLVEVAT GDMGPGKWRQ VDIEVYLPSE GRYRETHSCS
360 370 380 390 400
ALLDWQARRA NLRYRDPEGR VRYAYTLNNT ALATPRILAM LLENHQLQDG
410 420
RVRVPQALIP YMGKEVLEPC G
Length:421
Mass (Da):47,813
Last modified:May 23, 2004 - v2
Checksum:i5E89B0D131EFC209
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017221 Genomic DNA. Translation: AAS80868.1.
RefSeqiWP_011172965.1. NC_005835.1.
YP_004495.1. NC_005835.1.

Genome annotation databases

EnsemblBacteriaiAAS80868; AAS80868; TT_C0520.
KEGGitth:TTC0520.
PATRICi23951447. VBITheThe54392_0520.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017221 Genomic DNA. Translation: AAS80868.1.
RefSeqiWP_011172965.1. NC_005835.1.
YP_004495.1. NC_005835.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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/B94-419[»]
DisProtiDP00514.
ProteinModelPortaliP34945.
SMRiP34945. Positions 1-421.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi262724.TTC0520.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS80868; AAS80868; TT_C0520.
KEGGitth:TTC0520.
PATRICi23951447. VBITheThe54392_0520.

Phylogenomic databases

eggNOGiCOG0172.
KOiK01875.
OMAiFADDMFR.
OrthoDBiEOG61KBH9.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.
BioCyciTTHE262724:GCAT-532-MONOMER.
BRENDAi6.1.1.11. 2305.

Miscellaneous databases

EvolutionaryTraceiP34945.

Family and domain databases

Gene3Di1.10.287.40. 1 hit.
HAMAPiMF_00176. Ser_tRNA_synth_type1.
InterProiIPR002314. 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]
PANTHERiPTHR11778. PTHR11778. 1 hit.
PfamiPF02403. Seryl_tRNA_N. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
PIRSFiPIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
PRINTSiPR00981. TRNASYNTHSER.
SUPFAMiSSF46589. SSF46589. 1 hit.
TIGRFAMsiTIGR00414. serS. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. 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(1992) [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(1993) [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(1993) [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(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH TRNA(SER) AND SUBSTRATE ANALOG, SUBUNIT.

Entry informationi

Entry nameiSYS_THET2
AccessioniPrimary (citable) accession number: P34945
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 31, 1994
Last sequence update: May 23, 2004
Last modified: March 31, 2015
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.