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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)DescriptionActionsGraphical viewLength
Binding sitei285SerineUniRule annotation1
Binding sitei385SerineUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi262 – 264ATPUniRule annotation3
Nucleotide bindingi349 – 352ATPUniRule 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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001219951 – 425Serine--tRNA ligaseAdd BLAST425

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi224324.aq_298.

Structurei

Secondary structure

1425
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 9Combined sources6
Helixi11 – 18Combined sources8
Turni19 – 21Combined sources3
Helixi23 – 25Combined sources3
Helixi26 – 59Combined sources34
Helixi62 – 64Combined sources3
Turni70 – 72Combined sources3
Helixi76 – 103Combined sources28
Helixi119 – 121Combined sources3
Beta strandi123 – 129Combined sources7
Helixi141 – 147Combined sources7
Helixi153 – 160Combined sources8
Beta strandi166 – 168Combined sources3
Helixi170 – 188Combined sources19
Beta strandi192 – 195Combined sources4
Beta strandi198 – 200Combined sources3
Helixi202 – 208Combined sources7
Turni211 – 214Combined sources4
Helixi215 – 217Combined sources3
Turni222 – 224Combined sources3
Helixi233 – 237Combined sources5
Helixi238 – 240Combined sources3
Beta strandi243 – 246Combined sources4
Turni247 – 249Combined sources3
Beta strandi252 – 261Combined sources10
Beta strandi269 – 271Combined sources3
Beta strandi273 – 277Combined sources5
Beta strandi279 – 290Combined sources12
Helixi292 – 294Combined sources3
Helixi295 – 313Combined sources19
Beta strandi317 – 321Combined sources5
Turni324 – 326Combined sources3
Beta strandi332 – 341Combined sources10
Helixi342 – 344Combined sources3
Beta strandi346 – 355Combined sources10
Helixi359 – 364Combined sources6
Beta strandi366 – 369Combined sources4
Turni371 – 373Combined sources3
Beta strandi375 – 378Combined sources4
Beta strandi380 – 388Combined sources9
Helixi389 – 399Combined sources11
Turni411 – 413Combined sources3
Helixi414 – 417Combined sources4
Beta strandi420 – 422Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO66647.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni231 – 233Serine 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

eggNOGiENOG4105CGR. Bacteria.
COG0172. LUCA.
HOGENOMiHOG000035937.
InParanoidiO66647.
KOiK01875.
OMAiYRPERHE.
OrthoDBiPOG091H01YY.

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. 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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DQ3X-ray3.00A/B1-425[»]
ProteinModelPortaliO66647.
SMRiO66647.
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.
OrthoDBiPOG091H01YY.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.

Miscellaneous databases

EvolutionaryTraceiO66647.

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. 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...

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 2, 2016
This is version 104 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.