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Protein

O-phosphoseryl-tRNA(Sec) selenium transferase

Gene

spcS

Organism
Methanococcus maripaludis (strain S2 / LL)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.1 Publication

Catalytic activityi

O-phospho-L-seryl-tRNA(Sec) + selenophosphate + H2O = L-selenocysteinyl-tRNA(Sec) + 2 phosphate.1 Publication

Cofactori

pyridoxal 5'-phosphate1 Publication

Pathwayi: selenocysteinyl-tRNA(Sec) biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes selenocysteinyl-tRNA(Sec) from L-seryl-tRNA(Sec) (archaeal/eukaryal route).1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. L-seryl-tRNA(Sec) kinase (pstK)
  2. O-phosphoseryl-tRNA(Sec) selenium transferase (spcS)
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 selenocysteinyl-tRNA(Sec) from L-seryl-tRNA(Sec) (archaeal/eukaryal route), the pathway selenocysteinyl-tRNA(Sec) biosynthesis and in Aminoacyl-tRNA biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei71May act as a substrate filter by repelling compounds with a negatively charged alpha-carboxylateBy similarity1
Binding sitei72Pyridoxal phosphate1 Publication1
Binding sitei94Substrate1 Publication1
Binding sitei95Substrate1 Publication1
Binding sitei102Substrate1 Publication1
Binding sitei307Substrate1 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Pyridoxal phosphate, RNA-binding, Selenium, tRNA-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-14963.
BRENDAi2.9.1.2. 3262.
UniPathwayiUPA00906; UER00898.

Names & Taxonomyi

Protein namesi
Recommended name:
O-phosphoseryl-tRNA(Sec) selenium transferase (EC:2.9.1.21 Publication)
Alternative name(s):
Selenocysteine synthase
Short name:
Sec synthase
Selenocysteinyl-tRNA(Sec) synthase
Sep-tRNA:Sec-tRNA synthase
Short name:
SepSecS
Gene namesi
Name:spcS
Ordered Locus Names:MMP0595
OrganismiMethanococcus maripaludis (strain S2 / LL)
Taxonomic identifieri267377 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanococcaceaeMethanococcus
Proteomesi
  • UP000000590 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi72R → A: Loss of activity. 1 Publication1
Mutagenesisi94R → A: Loss of activity. 1 Publication1
Mutagenesisi247N → A: Reduced activity. 1 Publication1
Mutagenesisi278K → A: Loss of activity. 1 Publication1
Mutagenesisi307R → A: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002198831 – 436O-phosphoseryl-tRNA(Sec) selenium transferaseAdd BLAST436

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei278N6-(pyridoxal phosphate)lysine2 Publications1

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi267377.MMP0595.

Structurei

Secondary structure

1436
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 10Combined sources3
Helixi12 – 25Combined sources14
Helixi27 – 35Combined sources9
Helixi45 – 56Combined sources12
Helixi60 – 62Combined sources3
Helixi79 – 84Combined sources6
Turni85 – 87Combined sources3
Beta strandi92 – 94Combined sources3
Helixi106 – 125Combined sources20
Beta strandi131 – 137Combined sources7
Helixi139 – 154Combined sources16
Beta strandi158 – 162Combined sources5
Helixi167 – 175Combined sources9
Beta strandi179 – 183Combined sources5
Beta strandi186 – 188Combined sources3
Beta strandi191 – 193Combined sources3
Helixi196 – 208Combined sources13
Beta strandi213 – 220Combined sources8
Helixi230 – 240Combined sources11
Beta strandi244 – 247Combined sources4
Turni249 – 253Combined sources5
Helixi255 – 265Combined sources11
Beta strandi270 – 275Combined sources6
Helixi276 – 280Combined sources5
Beta strandi287 – 292Combined sources6
Helixi294 – 301Combined sources8
Helixi311 – 352Combined sources42
Beta strandi363 – 369Combined sources7
Helixi374 – 383Combined sources10
Beta strandi386 – 388Combined sources3
Beta strandi390 – 392Combined sources3
Helixi397 – 400Combined sources4
Beta strandi410 – 414Combined sources5
Helixi421 – 432Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Z67X-ray2.50A/B/C/D1-436[»]
ProteinModelPortaliQ6LZM9.
SMRiQ6LZM9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ6LZM9.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 44TetramerizationBy similarityAdd BLAST44
Regioni93 – 103Phosphate loop (P-loop)By similarityAdd BLAST11

Sequence similaritiesi

Belongs to the SepSecS family.Curated

Phylogenomic databases

eggNOGiarCOG00119. Archaea.
COG0076. LUCA.
HOGENOMiHOG000254245.
KOiK03341.
OMAiHIINGAY.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
InterProiIPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR019872. Sec-tRNA_Se_transferase.
IPR008829. SepSecS/SepCysS.
[Graphical view]
PANTHERiPTHR12944. PTHR12944. 1 hit.
PfamiPF05889. SepSecS. 1 hit.
[Graphical view]
PIRSFiPIRSF017689. SepSecS. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR03531. selenium_SpcS. 1 hit.

Sequencei

Sequence statusi: Complete.

Q6LZM9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLDFNIEGLI PKNMEKRGEL VLNEYLKEIE DVFNHRKIPE NGIDDEKIKL
60 70 80 90 100
FLKFLSMMDT DKDPKSVRIG EREARTYSKI HEELSSGFCH GIGRSGNLVD
110 120 130 140 150
PQPKASGASI MYALTNKILE SFFKQLGLNV HAIATPISTG MSISLCLSAA
160 170 180 190 200
RKKYGSNVVI YPYASHKSPI KAVSFVGMNM RLVETVLDGD RVYVPVEDIE
210 220 230 240 250
NAIKKEIELG NRPCVLSTLT FFPPRNSDDI VEIAKICENY DIPHIINGAY
260 270 280 290 300
AIQNNYYLEK LKKAFKYRVD AVVSSSDKNL LTPIGGGLVY STDAEFIKEI
310 320 330 340 350
SLSYPGRASA TPVVNTLVSL LSMGSKNYLE LVKNQKNSKK LLDELLNDLS
360 370 380 390 400
KKTGGKFLDV ESPIASCISV NSDPVEIAAK LYNLRVTGPR GIKKTDHFGN
410 420 430
CYLGTYTHDY IVMNAAIGVR TEDIVNSVSK LEKILL
Length:436
Mass (Da):48,447
Last modified:July 5, 2004 - v1
Checksum:i6B7CB252D5ABE6A0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX950229 Genomic DNA. Translation: CAF30151.1.
RefSeqiWP_011170539.1. NC_005791.1.

Genome annotation databases

EnsemblBacteriaiCAF30151; CAF30151; MMP0595.
GeneIDi2762564.
KEGGimmp:MMP0595.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX950229 Genomic DNA. Translation: CAF30151.1.
RefSeqiWP_011170539.1. NC_005791.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Z67X-ray2.50A/B/C/D1-436[»]
ProteinModelPortaliQ6LZM9.
SMRiQ6LZM9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi267377.MMP0595.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAF30151; CAF30151; MMP0595.
GeneIDi2762564.
KEGGimmp:MMP0595.

Phylogenomic databases

eggNOGiarCOG00119. Archaea.
COG0076. LUCA.
HOGENOMiHOG000254245.
KOiK03341.
OMAiHIINGAY.

Enzyme and pathway databases

UniPathwayiUPA00906; UER00898.
BioCyciMetaCyc:MONOMER-14963.
BRENDAi2.9.1.2. 3262.

Miscellaneous databases

EvolutionaryTraceiQ6LZM9.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
InterProiIPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR019872. Sec-tRNA_Se_transferase.
IPR008829. SepSecS/SepCysS.
[Graphical view]
PANTHERiPTHR12944. PTHR12944. 1 hit.
PfamiPF05889. SepSecS. 1 hit.
[Graphical view]
PIRSFiPIRSF017689. SepSecS. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR03531. selenium_SpcS. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSPCS_METMP
AccessioniPrimary (citable) accession number: Q6LZM9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: July 5, 2004
Last modified: November 2, 2016
This is version 70 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.