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Protein

Serine--tRNA ligase

Gene

serS

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 3 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 sitei285 – 2851SerineUniRule annotation
Binding sitei385 – 3851SerineUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi262 – 2643ATPUniRule annotation
Nucleotide bindingi349 – 3524ATPUniRule 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

BioCyciAAEO224324:GJBH-223-MONOMER.
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:aq_298
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 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 – 425425Serine--tRNA ligasePRO_0000121995Add
BLAST

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi224324.aq_298.

Structurei

Secondary structure

1
425
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 96Combined sources
Helixi11 – 188Combined sources
Turni19 – 213Combined sources
Helixi23 – 253Combined sources
Helixi26 – 5934Combined sources
Helixi62 – 643Combined sources
Turni70 – 723Combined sources
Helixi76 – 10328Combined sources
Helixi119 – 1213Combined sources
Beta strandi123 – 1297Combined sources
Helixi141 – 1477Combined sources
Helixi153 – 1608Combined sources
Beta strandi166 – 1683Combined sources
Helixi170 – 18819Combined sources
Beta strandi192 – 1954Combined sources
Beta strandi198 – 2003Combined sources
Helixi202 – 2087Combined sources
Turni211 – 2144Combined sources
Helixi215 – 2173Combined sources
Turni222 – 2243Combined sources
Helixi233 – 2375Combined sources
Helixi238 – 2403Combined sources
Beta strandi243 – 2464Combined sources
Turni247 – 2493Combined sources
Beta strandi252 – 26110Combined sources
Beta strandi269 – 2713Combined sources
Beta strandi273 – 2775Combined sources
Beta strandi279 – 29012Combined sources
Helixi292 – 2943Combined sources
Helixi295 – 31319Combined sources
Beta strandi317 – 3215Combined sources
Turni324 – 3263Combined sources
Beta strandi332 – 34110Combined sources
Helixi342 – 3443Combined sources
Beta strandi346 – 35510Combined sources
Helixi359 – 3646Combined sources
Beta strandi366 – 3694Combined sources
Turni371 – 3733Combined sources
Beta strandi375 – 3784Combined sources
Beta strandi380 – 3889Combined sources
Helixi389 – 39911Combined sources
Turni411 – 4133Combined sources
Helixi414 – 4174Combined sources
Beta strandi420 – 4223Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DQ3X-ray3.00A/B1-425[»]
ProteinModelPortaliO66647.
SMRiO66647. Positions 1-425.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO66647.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni231 – 2333Serine 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

eggNOGiENOG4105CGR. Bacteria.
COG0172. LUCA.
HOGENOMiHOG000035937.
InParanoidiO66647.
KOiK01875.
OMAiYRPERHE.
OrthoDBiEOG61KBH9.

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. 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.

O66647-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIDINLIREK PDYVKERLAT RDKELVSLVD KVLELDKRRR EIIKRLEALR
60 70 80 90 100
SERNKLSKEI GKLKREGKDT TEIQNRVKEL KEEIDRLEEE LRKVEEELKN
110 120 130 140 150
TLLWIPNLPH PSVPVGEDEK DNVEVRRWGE PRKFDFEPKP HWEIGERLGI
160 170 180 190 200
LDFKRGAKLS GSRFTVIAGW GARLERALIN FMLDLHTKKG YKEICPPHLV
210 220 230 240 250
KPEILIGTGQ LPKFEEDLYK CERDNLYLIP TAEVPLTNLY REEILKEENL
260 270 280 290 300
PIYLTAYTPC YRREAGAYGK DIRGIIRQHQ FDKVELVKIV HPDTSYDELE
310 320 330 340 350
KLVKDAEEVL QLLGLPYRVV ELCTGDLGFS AAKTYDIEVW FPSQNKYREI
360 370 380 390 400
SSCSNCEDFQ ARRMNTRFKD SKTGKNRFVH TLNGSGLAVG RTLAAILENY
410 420
QQEDGSVVVP EVLRDYVGTD VIRPE
Length:425
Mass (Da):49,433
Last modified:August 1, 1998 - v1
Checksum:i30173C92567DC784
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06595.1.
PIRiC70327.
RefSeqiNP_213207.1. NC_000918.1.
WP_010880145.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC06595; AAC06595; aq_298.
GeneIDi1192881.
KEGGiaae:aq_298.
PATRICi20958212. VBIAquAeo85532_0245.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06595.1.
PIRiC70327.
RefSeqiNP_213207.1. NC_000918.1.
WP_010880145.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DQ3X-ray3.00A/B1-425[»]
ProteinModelPortaliO66647.
SMRiO66647. Positions 1-425.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_298.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC06595; AAC06595; aq_298.
GeneIDi1192881.
KEGGiaae:aq_298.
PATRICi20958212. VBIAquAeo85532_0245.

Phylogenomic databases

eggNOGiENOG4105CGR. Bacteria.
COG0172. LUCA.
HOGENOMiHOG000035937.
InParanoidiO66647.
KOiK01875.
OMAiYRPERHE.
OrthoDBiEOG61KBH9.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.
BioCyciAAEO224324:GJBH-223-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO66647.

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. 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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: VF5.

Entry informationi

Entry nameiSYS_AQUAE
AccessioniPrimary (citable) accession number: O66647
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: August 1, 1998
Last modified: November 11, 2015
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference 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.