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Protein

Type-2 serine--tRNA ligase

Gene

serS

Organism
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
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

Cofactori

Zn2+UniRule annotationNote: Binds 1 Zn2+ ion per subunit. This ion is coordinated with 2 cysteines, 1 glutamate and a water molecule that dissociates from the zinc ion to allow the coordination of the amino group of the serine substrate, which is essential for catalysis.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. Type-2 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 sitei317Serine; via carbonyl oxygenUniRule annotation1
Metal bindingi319Zinc; catalyticUniRule annotation1
Binding sitei349SerineUniRule annotation1
Metal bindingi368Zinc; catalyticUniRule annotation1
Metal bindingi478Zinc; catalyticUniRule annotation1
Binding sitei485ATPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi349 – 351ATPUniRule annotation3
Nucleotide bindingi360 – 361ATPUniRule annotation2

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, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.

Names & Taxonomyi

Protein namesi
Recommended name:
Type-2 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:MK1460
OrganismiMethanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Taxonomic identifieri190192 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanopyriMethanopyralesMethanopyraceaeMethanopyrus
Proteomesi
  • UP000001826 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_00002861691 – 527Type-2 serine--tRNA ligaseAdd BLAST527

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi190192.MK1460.

Structurei

Secondary structure

1527
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 15Combined sources14
Helixi19 – 35Combined sources17
Helixi37 – 39Combined sources3
Beta strandi50 – 56Combined sources7
Beta strandi58 – 71Combined sources14
Helixi73 – 92Combined sources20
Beta strandi96 – 109Combined sources14
Helixi116 – 119Combined sources4
Beta strandi126 – 130Combined sources5
Beta strandi132 – 141Combined sources10
Helixi144 – 148Combined sources5
Helixi151 – 163Combined sources13
Turni164 – 167Combined sources4
Helixi169 – 171Combined sources3
Beta strandi181 – 184Combined sources4
Helixi196 – 202Combined sources7
Beta strandi205 – 208Combined sources4
Beta strandi215 – 217Combined sources3
Helixi219 – 235Combined sources17
Turni236 – 241Combined sources6
Beta strandi249 – 252Combined sources4
Helixi253 – 258Combined sources6
Helixi261 – 264Combined sources4
Helixi266 – 268Combined sources3
Helixi279 – 292Combined sources14
Helixi297 – 305Combined sources9
Beta strandi312 – 314Combined sources3
Beta strandi316 – 318Combined sources3
Helixi321 – 326Combined sources6
Turni333 – 335Combined sources3
Beta strandi338 – 342Combined sources5
Beta strandi345 – 348Combined sources4
Beta strandi358 – 360Combined sources3
Beta strandi362 – 373Combined sources12
Helixi375 – 395Combined sources21
Beta strandi400 – 404Combined sources5
Beta strandi412 – 414Combined sources3
Helixi415 – 418Combined sources4
Beta strandi428 – 434Combined sources7
Helixi436 – 438Combined sources3
Helixi444 – 446Combined sources3
Beta strandi447 – 457Combined sources11
Helixi459 – 463Combined sources5
Beta strandi467 – 470Combined sources4
Beta strandi475 – 482Combined sources8
Helixi483 – 494Combined sources12
Helixi498 – 500Combined sources3
Helixi503 – 513Combined sources11
Beta strandi523 – 525Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3W3SX-ray3.10A1-527[»]
ProteinModelPortaliQ8TVD2.
SMRiQ8TVD2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni366 – 368Serine bindingUniRule annotation3

Domaini

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

Sequence similaritiesi

Belongs to the class-II aminoacyl-tRNA synthetase family. Type-2 seryl-tRNA synthetase subfamily.UniRule annotation

Phylogenomic databases

eggNOGiarCOG00403. Archaea.
COG0172. LUCA.
HOGENOMiHOG000254149.
KOiK01875.
OMAiAQCEPFY.

Family and domain databases

HAMAPiMF_01278. Ser_tRNA_synth_type2. 1 hit.
InterProiIPR002314. aa-tRNA-synt_IIb.
IPR006195. aa-tRNA-synth_II.
IPR004503. Ser-tRNA-ligase_IIa_arc.
[Graphical view]
PfamiPF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00415. serS_MJ. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8TVD2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELKFSAEVE LTLSREVDPA EIEPTVEEFV KEANEDLLQR GVPTGKEGAK
60 70 80 90 100
IESYRVLEDT IEMEITGTRY LRPHEAAMRV RKRLAERLGR KHRVGVRDLK
110 120 130 140 150
IPRYEVVLRF DREVTRDDVG YVPVADDVVV EDGTVRLTFQ DVDEEMLRRH
160 170 180 190 200
VIDRVIRLVA WAVEERSELV ERVTKVEPGT VVDESGPREI RFDGDVTEEA
210 220 230 240 250
RRRGWVKEFP GRGQWIYTPP MAALFEVLRD FLLERVTRKL GFEPALFPKL
260 270 280 290 300
IPLETMFRMR YLHGLPDGMY YVCPPKRDPE LFDDFKRELY VWGELNERTL
310 320 330 340 350
GSLKEKLRDP GYVLAPAQCE PFYELLRDEV VDPERLPIKL YDCSGWTYRW
360 370 380 390 400
EGGAAKGLER VNEFQRIEHV WIAEPEEAER IREELLEATK RVAEELELEW
410 420 430 440 450
KVVVSDDPFY LEGRLLEDRD IELPDVPSYE FEVYLPFKGE RSSEEAWISV
460 470 480 490 500
GSFNVHGEHF VDGFNVKEKS GRTLFTGCAG LGVTRWVVGL LAQHGFEPEE
510 520
WPEPILERID EKFGGLPEVP KTLTWPE
Length:527
Mass (Da):61,368
Last modified:June 1, 2002 - v1
Checksum:i7526147D81EFC5CD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009439 Genomic DNA. Translation: AAM02673.1.

Genome annotation databases

EnsemblBacteriaiAAM02673; AAM02673; MK1460.
KEGGimka:MK1460.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009439 Genomic DNA. Translation: AAM02673.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3W3SX-ray3.10A1-527[»]
ProteinModelPortaliQ8TVD2.
SMRiQ8TVD2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi190192.MK1460.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM02673; AAM02673; MK1460.
KEGGimka:MK1460.

Phylogenomic databases

eggNOGiarCOG00403. Archaea.
COG0172. LUCA.
HOGENOMiHOG000254149.
KOiK01875.
OMAiAQCEPFY.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.

Family and domain databases

HAMAPiMF_01278. Ser_tRNA_synth_type2. 1 hit.
InterProiIPR002314. aa-tRNA-synt_IIb.
IPR006195. aa-tRNA-synth_II.
IPR004503. Ser-tRNA-ligase_IIa_arc.
[Graphical view]
PfamiPF00587. tRNA-synt_2b. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00415. serS_MJ. 1 hit.
PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSYS2_METKA
AccessioniPrimary (citable) accession number: Q8TVD2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: June 1, 2002
Last modified: November 2, 2016
This is version 85 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.