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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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei317 – 3171Serine; via carbonyl oxygenUniRule annotation
Metal bindingi319 – 3191Zinc; catalyticUniRule annotation
Binding sitei349 – 3491SerineUniRule annotation
Metal bindingi368 – 3681Zinc; catalyticUniRule annotation
Metal bindingi478 – 4781Zinc; catalyticUniRule annotation
Binding sitei485 – 4851ATPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi349 – 3513ATPUniRule annotation
Nucleotide bindingi360 – 3612ATPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. serine-tRNA ligase activity Source: UniProtKB-HAMAP
  3. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. selenocysteine biosynthetic process Source: UniProtKB-HAMAP
  2. selenocysteinyl-tRNA(Sec) biosynthetic process Source: UniProtKB-UniPathway
  3. seryl-tRNA aminoacylation Source: UniProtKB-HAMAP
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
ProteomesiUP000001826 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 527527Type-2 serine--tRNA ligasePRO_0000286169Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi190192.MK1460.

Structurei

Secondary structure

1
527
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 1514Combined sources
Helixi19 – 3517Combined sources
Helixi37 – 393Combined sources
Beta strandi50 – 567Combined sources
Beta strandi58 – 7114Combined sources
Helixi73 – 9220Combined sources
Beta strandi96 – 10914Combined sources
Helixi116 – 1194Combined sources
Beta strandi126 – 1305Combined sources
Beta strandi132 – 14110Combined sources
Helixi144 – 1485Combined sources
Helixi151 – 16313Combined sources
Turni164 – 1674Combined sources
Helixi169 – 1713Combined sources
Beta strandi181 – 1844Combined sources
Helixi196 – 2027Combined sources
Beta strandi205 – 2084Combined sources
Beta strandi215 – 2173Combined sources
Helixi219 – 23517Combined sources
Turni236 – 2416Combined sources
Beta strandi249 – 2524Combined sources
Helixi253 – 2586Combined sources
Helixi261 – 2644Combined sources
Helixi266 – 2683Combined sources
Helixi279 – 29214Combined sources
Helixi297 – 3059Combined sources
Beta strandi312 – 3143Combined sources
Beta strandi316 – 3183Combined sources
Helixi321 – 3266Combined sources
Turni333 – 3353Combined sources
Beta strandi338 – 3425Combined sources
Beta strandi345 – 3484Combined sources
Beta strandi358 – 3603Combined sources
Beta strandi362 – 37312Combined sources
Helixi375 – 39521Combined sources
Beta strandi400 – 4045Combined sources
Beta strandi412 – 4143Combined sources
Helixi415 – 4184Combined sources
Beta strandi428 – 4347Combined sources
Helixi436 – 4383Combined sources
Helixi444 – 4463Combined sources
Beta strandi447 – 45711Combined sources
Helixi459 – 4635Combined sources
Beta strandi467 – 4704Combined sources
Beta strandi475 – 4828Combined sources
Helixi483 – 49412Combined sources
Helixi498 – 5003Combined sources
Helixi503 – 51311Combined sources
Beta strandi523 – 5253Combined sources

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni366 – 3683Serine bindingUniRule annotation

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

eggNOGiCOG0172.
HOGENOMiHOG000254149.
KOiK01875.
OMAiAQCEPFY.

Family and domain databases

HAMAPiMF_01278. Ser_tRNA_synth_type2.
InterProiIPR002314. aa-tRNA-synt_IIb_cons-dom.
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.
RefSeqiNP_614743.1. NC_003551.1.

Genome annotation databases

EnsemblBacteriaiAAM02673; AAM02673; MK1460.
GeneIDi1478055.
KEGGimka:MK1460.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009439 Genomic DNA. Translation: AAM02673.1.
RefSeqiNP_614743.1. NC_003551.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi190192.MK1460.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM02673; AAM02673; MK1460.
GeneIDi1478055.
KEGGimka:MK1460.

Phylogenomic databases

eggNOGiCOG0172.
HOGENOMiHOG000254149.
KOiK01875.
OMAiAQCEPFY.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00895.

Family and domain databases

HAMAPiMF_01278. Ser_tRNA_synth_type2.
InterProiIPR002314. aa-tRNA-synt_IIb_cons-dom.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.

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: February 4, 2015
This is version 81 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

External Data

Dasty 3

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 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.