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Protein

Serine--tRNA ligase

Gene

serS

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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).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: selenocysteinyl-tRNA(Sec) biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec).UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Serine--tRNA ligase (serS)
This subpathway is part of the pathway selenocysteinyl-tRNA(Sec) biosynthesis, which is itself part of Aminoacyl-tRNA biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-seryl-tRNA(Sec) from L-serine and tRNA(Sec), the pathway selenocysteinyl-tRNA(Sec) biosynthesis and in Aminoacyl-tRNA biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei299ATP; via amide nitrogen and carbonyl oxygenUniRule annotation1
Binding sitei306SerineUniRule annotation1
Binding sitei406SerineUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi283 – 285ATPUniRule annotation3
Nucleotide bindingi370 – 373ATPUniRule annotation4

GO - Molecular functioni

GO - Biological processi

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

BRENDAi6.1.1.11. 5244.
UniPathwayiUPA00906; UER00895.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine--tRNA ligaseUniRule annotation (EC:6.1.1.11UniRule annotation)
Alternative name(s):
Seryl-tRNA synthetaseUniRule annotation
Short name:
SerRSUniRule annotation
Seryl-tRNA(Ser/Sec) synthetaseUniRule annotation
Gene namesi
Name:serSUniRule annotation
Ordered Locus Names:PH0710
ORF Names:PHCF014
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001221821 – 455Serine--tRNA ligaseAdd BLAST455

Interactioni

Subunit structurei

Homodimer. The tRNA molecule binds across the dimer.UniRule annotation

Protein-protein interaction databases

STRINGi70601.PH0710.

Structurei

Secondary structure

1455
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 9Combined sources6
Helixi11 – 21Combined sources11
Helixi24 – 28Combined sources5
Helixi29 – 65Combined sources37
Helixi72 – 103Combined sources32
Helixi120 – 122Combined sources3
Beta strandi124 – 130Combined sources7
Beta strandi132 – 135Combined sources4
Helixi136 – 138Combined sources3
Helixi139 – 146Combined sources8
Beta strandi152 – 157Combined sources6
Helixi162 – 168Combined sources7
Beta strandi172 – 174Combined sources3
Helixi175 – 180Combined sources6
Beta strandi187 – 189Combined sources3
Helixi190 – 209Combined sources20
Beta strandi213 – 216Combined sources4
Beta strandi219 – 221Combined sources3
Helixi223 – 227Combined sources5
Helixi234 – 237Combined sources4
Beta strandi240 – 242Combined sources3
Helixi254 – 259Combined sources6
Turni260 – 263Combined sources4
Beta strandi264 – 267Combined sources4
Turni268 – 270Combined sources3
Beta strandi272 – 282Combined sources11
Beta strandi289 – 292Combined sources4
Beta strandi295 – 298Combined sources4
Beta strandi300 – 311Combined sources12
Turni313 – 315Combined sources3
Helixi316 – 333Combined sources18
Beta strandi338 – 342Combined sources5
Helixi345 – 347Combined sources3
Beta strandi353 – 362Combined sources10
Turni363 – 366Combined sources4
Beta strandi367 – 376Combined sources10
Turni378 – 381Combined sources4
Helixi382 – 385Combined sources4
Beta strandi387 – 392Combined sources6
Beta strandi401 – 409Combined sources9
Helixi410 – 420Combined sources11
Helixi432 – 434Combined sources3
Helixi435 – 438Combined sources4
Beta strandi441 – 443Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DQ0X-ray2.60A/B1-455[»]
2ZR2X-ray2.80A/B1-455[»]
2ZR3X-ray3.00A/B1-455[»]
ProteinModelPortaliO58441.
SMRiO58441.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58441.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni252 – 254Serine bindingUniRule annotation3

Domaini

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

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG00403. Archaea.
COG0172. LUCA.
HOGENOMiHOG000035937.
KOiK01875.
OMAiYRPERHE.

Family and domain databases

CDDicd00770. SerRS_core. 1 hit.
Gene3Di1.10.287.40. 1 hit.
HAMAPiMF_00176. Ser_tRNA_synth_type1. 1 hit.
InterProiIPR002314. aa-tRNA-synt_IIb.
IPR006195. aa-tRNA-synth_II.
IPR002317. Ser-tRNA-ligase_type_1.
IPR015866. Ser-tRNA-synth_1_N.
IPR033729. SerRS_core.
IPR010978. tRNA-bd_arm.
[Graphical view]
PANTHERiPTHR11778. PTHR11778. 2 hits.
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.

O58441-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLDIKLIREN PELVKNDLIK RGELEKVKWV DEILKLDTEW RTKLKEINRL
60 70 80 90 100
RHERNKIAVE IGKRRKKGEP VDELLAKSRE IVKRIGELEN EVEELKKKID
110 120 130 140 150
YYLWRLPNIT HPSVPVGKDE NDNVPIRFWG KARVWKGHLE RFLEQSQGKM
160 170 180 190 200
EYEILEWKPK LHVDLLEILG GADFARAAKV SGSRFYYLLN EIVILDLALI
210 220 230 240 250
RFALDRLIEK GFTPVIPPYM VRRFVEEGST SFEDFEDVIY KVEDEDLYLI
260 270 280 290 300
PTAEHPLAGM HANEILDGKD LPLLYVGVSP CFRKEAGTAG KDTKGIFRVH
310 320 330 340 350
QFHKVEQFVY SRPEESWEWH EKIIRNAEEL FQELEIPYRV VNICTGDLGY
360 370 380 390 400
VAAKKYDIEA WMPGQGKFRE VVSASNCTDW QARRLNIRFR DRTDEKPRYV
410 420 430 440 450
HTLNSTAIAT SRAIVAILEN HQEEDGTVRI PKVLWKYTGF KEIVPVEKKE

RCCAT
Length:455
Mass (Da):53,255
Last modified:May 30, 2000 - v2
Checksum:iB8D8A418A0651710
GO

Sequence cautioni

The sequence BAA29801 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29801.1. Different initiation.
PIRiG71117.
RefSeqiWP_048053201.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA29801; BAA29801; BAA29801.
GeneIDi1443040.
KEGGipho:PH0710.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29801.1. Different initiation.
PIRiG71117.
RefSeqiWP_048053201.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DQ0X-ray2.60A/B1-455[»]
2ZR2X-ray2.80A/B1-455[»]
2ZR3X-ray3.00A/B1-455[»]
ProteinModelPortaliO58441.
SMRiO58441.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0710.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29801; BAA29801; BAA29801.
GeneIDi1443040.
KEGGipho:PH0710.

Phylogenomic databases

eggNOGiarCOG00403. Archaea.
COG0172. LUCA.
HOGENOMiHOG000035937.
KOiK01875.
OMAiYRPERHE.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.
BRENDAi6.1.1.11. 5244.

Miscellaneous databases

EvolutionaryTraceiO58441.

Family and domain databases

CDDicd00770. SerRS_core. 1 hit.
Gene3Di1.10.287.40. 1 hit.
HAMAPiMF_00176. Ser_tRNA_synth_type1. 1 hit.
InterProiIPR002314. aa-tRNA-synt_IIb.
IPR006195. aa-tRNA-synth_II.
IPR002317. Ser-tRNA-ligase_type_1.
IPR015866. Ser-tRNA-synth_1_N.
IPR033729. SerRS_core.
IPR010978. tRNA-bd_arm.
[Graphical view]
PANTHERiPTHR11778. PTHR11778. 2 hits.
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...

Entry informationi

Entry nameiSYS_PYRHO
AccessioniPrimary (citable) accession number: O58441
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: May 30, 2000
Last modified: November 2, 2016
This is version 108 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

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 one 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.