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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei299 – 2991ATP; via amide nitrogen and carbonyl oxygenUniRule annotation
Binding sitei306 – 3061SerineUniRule annotation
Binding sitei406 – 4061SerineUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi283 – 2853ATPUniRule annotation
Nucleotide bindingi370 – 3734ATPUniRule annotation

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

BioCyciPHOR70601:GJWR-706-MONOMER.
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 455455Serine--tRNA ligasePRO_0000122182Add
BLAST

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi70601.PH0710.

Structurei

Secondary structure

1
455
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 96Combined sources
Helixi11 – 2111Combined sources
Helixi24 – 285Combined sources
Helixi29 – 6537Combined sources
Helixi72 – 10332Combined sources
Helixi120 – 1223Combined sources
Beta strandi124 – 1307Combined sources
Beta strandi132 – 1354Combined sources
Helixi136 – 1383Combined sources
Helixi139 – 1468Combined sources
Beta strandi152 – 1576Combined sources
Helixi162 – 1687Combined sources
Beta strandi172 – 1743Combined sources
Helixi175 – 1806Combined sources
Beta strandi187 – 1893Combined sources
Helixi190 – 20920Combined sources
Beta strandi213 – 2164Combined sources
Beta strandi219 – 2213Combined sources
Helixi223 – 2275Combined sources
Helixi234 – 2374Combined sources
Beta strandi240 – 2423Combined sources
Helixi254 – 2596Combined sources
Turni260 – 2634Combined sources
Beta strandi264 – 2674Combined sources
Turni268 – 2703Combined sources
Beta strandi272 – 28211Combined sources
Beta strandi289 – 2924Combined sources
Beta strandi295 – 2984Combined sources
Beta strandi300 – 31112Combined sources
Turni313 – 3153Combined sources
Helixi316 – 33318Combined sources
Beta strandi338 – 3425Combined sources
Helixi345 – 3473Combined sources
Beta strandi353 – 36210Combined sources
Turni363 – 3664Combined sources
Beta strandi367 – 37610Combined sources
Turni378 – 3814Combined sources
Helixi382 – 3854Combined sources
Beta strandi387 – 3926Combined sources
Beta strandi401 – 4099Combined sources
Helixi410 – 42011Combined sources
Helixi432 – 4343Combined sources
Helixi435 – 4384Combined sources
Beta strandi441 – 4433Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DQ0X-ray2.60A/B1-455[»]
2ZR2X-ray2.80A/B1-455[»]
2ZR3X-ray3.00A/B1-455[»]
ProteinModelPortaliO58441.
SMRiO58441. Positions 1-448.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58441.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni252 – 2543Serine 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

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

Gene3Di1.10.287.40. 1 hit.
HAMAPiMF_00176. Ser_tRNA_synth_type1.
InterProiIPR002314. aa-tRNA-synt_IIb.
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. 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 BAA29801.1 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
EntryMethodResolution (Å)ChainPositionsPDBsum
2DQ0X-ray2.60A/B1-455[»]
2ZR2X-ray2.80A/B1-455[»]
2ZR3X-ray3.00A/B1-455[»]
ProteinModelPortaliO58441.
SMRiO58441. Positions 1-448.
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.
BioCyciPHOR70601:GJWR-706-MONOMER.
BRENDAi6.1.1.11. 5244.

Miscellaneous databases

EvolutionaryTraceiO58441.

Family and domain databases

Gene3Di1.10.287.40. 1 hit.
HAMAPiMF_00176. Ser_tRNA_synth_type1.
InterProiIPR002314. aa-tRNA-synt_IIb.
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. 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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
  2. "Crystal structure of PH0710."
    RIKEN structural genomics initiative (RSGI)
    Submitted (JUN-2007) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).

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 11, 2015
This is version 105 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.