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P34945

- SYS_THET2

UniProt

P34945 - SYS_THET2

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Protein

Serine--tRNA ligase

Gene
serS, TT_C0520
Organism
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Status
Reviewed - 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).UniRule annotation

Catalytic activityi

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

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 – 2583ATPUniRule annotation
Nucleotide bindingi345 – 3484ATPUniRule annotation

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.
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: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 421421Serine--tRNA ligaseUniRule annotationPRO_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 – 96
Helixi11 – 2111
Helixi27 – 5731
Beta strandi58 – 614
Helixi63 – 653
Helixi94 – 985
Beta strandi111 – 1133
Helixi114 – 1163
Beta strandi118 – 1247
Helixi136 – 1438
Helixi150 – 1545
Helixi163 – 18220
Beta strandi186 – 1894
Beta strandi192 – 1954
Helixi196 – 2027
Turni205 – 2084
Helixi209 – 2113
Turni216 – 2194
Beta strandi220 – 2223
Helixi227 – 2326
Turni233 – 2364
Beta strandi238 – 2403
Helixi241 – 2433
Beta strandi245 – 25511
Beta strandi268 – 2714
Beta strandi273 – 28412
Helixi288 – 30821
Beta strandi313 – 3175
Turni320 – 3223
Beta strandi328 – 33710
Helixi338 – 3403
Beta strandi342 – 35312
Helixi355 – 3606
Beta strandi363 – 3653
Beta strandi371 – 3733
Beta strandi375 – 38410
Helixi386 – 39510
Helixi406 – 4083
Helixi409 – 4124
Beta strandi413 – 4175

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiP34945.

Family & Domainsi

Region

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

Domaini

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0172.
KOiK01875.
OMAiNEGHNES.
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

MVDLKRLRQE PEVFHRAIRE KGVALDLEAL LALDREVQEL KKRLQEVQTE    50
RNQVAKRVPK APPEEKEALI ARGKALGEEA KRLEEALREK EARLEALLLQ 100
VPLPPWPGAP VGGEEANREI KRVGGPPEFS FPPLDHVALM EKNGWWEPRI 150
SQVSGSRSYA LKGDLALYEL ALLRFAMDFM ARRGFLPMTL PSYAREKAFL 200
GTGHFPAYRD QVWAIAETDL YLTGTAEVVL NALHSGEILP YEALPLRYAG 250
YAPAFRSEAG SFGKDVRGLM RVHQFHKVEQ YVLTEASLEA SDRAFQELLE 300
NAEEILRLLE LPYRLVEVAT GDMGPGKWRQ VDIEVYLPSE GRYRETHSCS 350
ALLDWQARRA NLRYRDPEGR VRYAYTLNNT ALATPRILAM LLENHQLQDG 400
RVRVPQALIP YMGKEVLEPC G 421
Length:421
Mass (Da):47,813
Last modified:May 24, 2004 - v2
Checksum:i5E89B0D131EFC209
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
GeneIDi2775083.
KEGGitth:TTC0520.
PATRICi23951447. VBITheThe54392_0520.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE017221 Genomic DNA. Translation: AAS80868.1 .
RefSeqi WP_011172965.1. NC_005835.1.
YP_004495.1. NC_005835.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1SER X-ray 2.90 A/B 1-421 [» ]
1SES X-ray 2.50 A/B 1-421 [» ]
1SET X-ray 2.55 A/B 1-421 [» ]
1SRY X-ray 2.50 A/B 1-421 [» ]
3ERR X-ray 2.27 A/B 94-419 [» ]
DisProti DP00514.
ProteinModelPortali P34945.
SMRi P34945. Positions 1-421.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 262724.TTC0520.

Chemistry

DrugBanki DB00131. Adenosine monophosphate.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAS80868 ; AAS80868 ; TT_C0520 .
GeneIDi 2775083.
KEGGi tth:TTC0520.
PATRICi 23951447. VBITheThe54392_0520.

Phylogenomic databases

eggNOGi COG0172.
KOi K01875.
OMAi NEGHNES.
OrthoDBi EOG61KBH9.

Enzyme and pathway databases

UniPathwayi UPA00906 ; UER00895 .
BioCyci TTHE262724:GCAT-532-MONOMER.

Miscellaneous databases

EvolutionaryTracei P34945.

Family and domain databases

Gene3Di 1.10.287.40. 1 hit.
HAMAPi MF_00176. Ser_tRNA_synth_type1.
InterProi 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 ]
PANTHERi PTHR11778. PTHR11778. 1 hit.
Pfami PF02403. Seryl_tRNA_N. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view ]
PIRSFi PIRSF001529. Ser-tRNA-synth_IIa. 1 hit.
PRINTSi PR00981. TRNASYNTHSER.
SUPFAMi SSF46589. SSF46589. 1 hit.
TIGRFAMsi TIGR00414. serS. 1 hit.
PROSITEi PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view ]
ProtoNeti Search...

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(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.

Entry informationi

Entry nameiSYS_THET2
AccessioniPrimary (citable) accession number: P34945
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: May 24, 2004
Last modified: September 3, 2014
This is version 110 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

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