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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)LengthDescriptionGraphical viewFeature identifierActions
Sitei71 – 711May act as a substrate filter by repelling compounds with a negatively charged alpha-carboxylateBy similarity
Binding sitei72 – 721Pyridoxal phosphate1 Publication
Binding sitei94 – 941Substrate1 Publication
Binding sitei95 – 951Substrate1 Publication
Binding sitei102 – 1021Substrate1 Publication
Binding sitei307 – 3071Substrate1 Publication

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.
MMAR267377:GJ77-623-MONOMER.
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi72 – 721R → A: Loss of activity. 1 Publication
Mutagenesisi94 – 941R → A: Loss of activity. 1 Publication
Mutagenesisi247 – 2471N → A: Reduced activity. 1 Publication
Mutagenesisi278 – 2781K → A: Loss of activity. 1 Publication
Mutagenesisi307 – 3071R → A: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 436436O-phosphoseryl-tRNA(Sec) selenium transferasePRO_0000219883Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei278 – 2781N6-(pyridoxal phosphate)lysine2 Publications

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi267377.MMP0595.

Structurei

Secondary structure

1
436
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 103Combined sources
Helixi12 – 2514Combined sources
Helixi27 – 359Combined sources
Helixi45 – 5612Combined sources
Helixi60 – 623Combined sources
Helixi79 – 846Combined sources
Turni85 – 873Combined sources
Beta strandi92 – 943Combined sources
Helixi106 – 12520Combined sources
Beta strandi131 – 1377Combined sources
Helixi139 – 15416Combined sources
Beta strandi158 – 1625Combined sources
Helixi167 – 1759Combined sources
Beta strandi179 – 1835Combined sources
Beta strandi186 – 1883Combined sources
Beta strandi191 – 1933Combined sources
Helixi196 – 20813Combined sources
Beta strandi213 – 2208Combined sources
Helixi230 – 24011Combined sources
Beta strandi244 – 2474Combined sources
Turni249 – 2535Combined sources
Helixi255 – 26511Combined sources
Beta strandi270 – 2756Combined sources
Helixi276 – 2805Combined sources
Beta strandi287 – 2926Combined sources
Helixi294 – 3018Combined sources
Helixi311 – 35242Combined sources
Beta strandi363 – 3697Combined sources
Helixi374 – 38310Combined sources
Beta strandi386 – 3883Combined sources
Beta strandi390 – 3923Combined sources
Helixi397 – 4004Combined sources
Beta strandi410 – 4145Combined sources
Helixi421 – 43212Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z67X-ray2.50A/B/C/D1-436[»]
ProteinModelPortaliQ6LZM9.
SMRiQ6LZM9. Positions 1-434.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ6LZM9.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 4444TetramerizationBy similarityAdd
BLAST
Regioni93 – 10311Phosphate loop (P-loop)By similarityAdd
BLAST

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z67X-ray2.50A/B/C/D1-436[»]
ProteinModelPortaliQ6LZM9.
SMRiQ6LZM9. Positions 1-434.
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.
MMAR267377:GJ77-623-MONOMER.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: S2 / LL.
  2. "RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea."
    Yuan J., Palioura S., Salazar J.C., Su D., O'Donoghue P., Hohn M.J., Cardoso A.M., Whitman W.B., Soell D.
    Proc. Natl. Acad. Sci. U.S.A. 103:18923-18927(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, PATHWAY, PYRIDOXAL PHOSPHATE AT LYS-278, MUTAGENESIS OF LYS-278.
  3. "Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation."
    Araiso Y., Palioura S., Ishitani R., Sherrer R.L., O'Donoghue P., Yuan J., Oshikane H., Domae N., Defranco J., Soll D., Nureki O.
    Nucleic Acids Res. 36:1187-1199(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE, SUBUNIT, MUTAGENESIS OF ARG-72; ARG-94; ASN-247 AND ARG-307.

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: January 20, 2016
This is version 68 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.