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P49903 (SPS1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 125. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Selenide, water dikinase 1

EC=2.7.9.3
Alternative name(s):
Selenium donor protein 1
Selenophosphate synthase 1
Gene names
Name:SEPHS1
Synonyms:SELD, SPS, SPS1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length392 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Synthesizes selenophosphate from selenide and ATP. Ref.1

Catalytic activity

ATP + selenide + H2O = AMP + selenophosphate + phosphate.

Enzyme regulation

Activated by phosphate ions and by potassium ions. Ref.11

Subunit structure

Homodimer (isoform 1, isoform 2, isoform 3 and isoform 4) Heterodimer of isoform 1 and isoform 3. Heterodimer of isoform 2 and isoform 4. Ref.2 Ref.11

Subcellular location

Isoform 1: Cell membrane. Nucleus membrane Ref.2.

Isoform 2: Cytoplasm Ref.2.

Isoform 3: Cytoplasm Ref.2.

Isoform 4: Cytoplasm Ref.2.

Tissue specificity

Isoform 1 and isoform 2 are gradually expressed during the cell cycle until G2/M phase and then decreased. Isoform 3 is gradually expressed during the cell cycle until S phase and then decreased. Ref.2

Sequence similarities

Belongs to the selenophosphate synthase 1 family. Class II subfamily.

Caution

The conserved active site Cys (or selenocysteine) residue in position 29 is replaced by a Thr. However, as function in selenoprotein synthesis is proven, it is possible Cys-31 is the active site.

Sequence caution

The sequence AAA87567.1 differs from that shown. Reason: Frameshift at position 377.

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P49903-1)

Also known as: Major type; MT;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P49903-2)

Also known as: Delta E8;

The sequence of this isoform differs from the canonical sequence as follows:
     251-321: Missing.
Isoform 3 (identifier: P49903-3)

Also known as: Delta E2;

The sequence of this isoform differs from the canonical sequence as follows:
     1-67: Missing.
Isoform 4 (identifier: P49903-4)

Also known as: E9 and E9a;

The sequence of this isoform differs from the canonical sequence as follows:
     322-392: GGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVATQNVNPTPGATS → DVQ

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.8
Chain2 – 392391Selenide, water dikinase 1
PRO_0000127648

Regions

Nucleotide binding67 – 693ATP
Nucleotide binding162 – 1643ATP; shared with dimeric partner
Nucleotide binding267 – 2737ATP

Sites

Active site311 Potential
Binding site321ATP
Binding site871ATP
Binding site1101ATP
Site321Important for catalytic activity By similarity

Amino acid modifications

Modified residue21N-acetylserine Ref.8

Natural variations

Alternative sequence1 – 6767Missing in isoform 3.
VSP_046701
Alternative sequence251 – 32171Missing in isoform 2.
VSP_046702
Alternative sequence322 – 39271GGLLI…PGATS → DVQ in isoform 4.
VSP_047451

Experimental info

Mutagenesis851T → A: Strongly reduced ADP hydrolysis. Ref.11
Mutagenesis2681G → C: No change in ATP-binding. Ref.1
Mutagenesis2701G → R: No change in ATP-binding. Ref.1
Mutagenesis2731G → A, D or V: Loss of ATP-binding. Ref.1
Mutagenesis2741H → N: Reduced ATP-binding. Ref.1
Mutagenesis2741H → Y: Increased ATP-binding. Ref.1
Sequence conflict2601A → T in AAA87567. Ref.1

Secondary structure

.................................................. 392
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Major type) (MT) [UniParc].

Last modified December 13, 2002. Version 2.
Checksum: E9636E38146D926D

FASTA39242,911
        10         20         30         40         50         60 
MSTRESFNPE SYELDKSFRL TRFTELKGTG CKVPQDVLQK LLESLQENHF QEDEQFLGAV 

        70         80         90        100        110        120 
MPRLGIGMDT CVIPLRHGGL SLVQTTDYIY PIVDDPYMMG RIACANVLSD LYAMGVTECD 

       130        140        150        160        170        180 
NMLMLLGVSN KMTDRERDKV MPLIIQGFKD AAEEAGTSVT GGQTVLNPWI VLGGVATTVC 

       190        200        210        220        230        240 
QPNEFIMPDN AVPGDVLVLT KPLGTQVAVA VHQWLDIPEK WNKIKLVVTQ EDVELAYQEA 

       250        260        270        280        290        300 
MMNMARLNRT AAGLMHTFNA HAATDITGFG ILGHAQNLAK QQRNEVSFVI HNLPVLAKMA 

       310        320        330        340        350        360 
AVSKACGNMF GLMHGTCPET SGGLLICLPR EQAARFCAEI KSPKYGEGHQ AWIIGIVEKG 

       370        380        390 
NRTARIIDKP RIIEVAPQVA TQNVNPTPGA TS 

« Hide

Isoform 2 (Delta E8) [UniParc].

Checksum: 1894C5DBC991ABA8
Show »

FASTA32135,479
Isoform 3 (Delta E2) [UniParc].

Checksum: 6938A3EB8339E631
Show »

FASTA32535,208
Isoform 4 (E9 and E9a) [UniParc].

Checksum: 538F17DE5C1D3644
Show »

FASTA32435,620

References

« Hide 'large scale' references
[1]"Cloning and functional characterization of human selenophosphate synthetase, an essential component of selenoprotein synthesis."
Low S.C., Harney J.W., Berry M.J.
J. Biol. Chem. 270:21659-21664(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, ATP-BINDING, MUTAGENESIS OF GLY-268; GLY-270; GLY-273 AND HIS-274.
Tissue: Liver.
[2]"Human selenophosphate synthetase 1 has five splice variants with unique interactions, subcellular localizations and expression patterns."
Kim J.Y., Lee K.H., Shim M.S., Shin H., Xu X.M., Carlson B.A., Hatfield D.L., Lee B.J.
Biochem. Biophys. Res. Commun. 397:53-58(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4), SUBUNIT, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
Tissue: Mammary gland.
[4]"The DNA sequence and comparative analysis of human chromosome 10."
Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. expand/collapse author list , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Placenta and PNS.
[7]Lubec G., Chen W.-Q., Sun Y.
Submitted (DEC-2008) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 5-16 AND 64-76, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Fetal brain cortex.
[8]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[9]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Crystal structures of catalytic intermediates of human selenophosphate synthetase 1."
Wang K.T., Wang J., Li L.F., Su X.D.
J. Mol. Biol. 390:747-759(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH ADP; MAGNESIUM IONS AND PHOSPHATE, SUBUNIT, ENZYME REGULATION, MUTAGENESIS OF THR-85.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U34044 mRNA. Translation: AAA87567.1. Frameshift.
GU954545 mRNA. Translation: ADF78120.1.
GU954546 mRNA. Translation: ADF78121.1.
GU954547 mRNA. Translation: ADF78122.1.
GU954548 mRNA. Translation: ADF78123.1.
GU954549 mRNA. Translation: ADF78124.1.
AK301568 mRNA. Translation: BAG63062.1.
AL138764, AL355870 Genomic DNA. Translation: CAI12907.1.
AL355870, AL138764 Genomic DNA. Translation: CAI14198.1.
CH471072 Genomic DNA. Translation: EAW86289.1.
CH471072 Genomic DNA. Translation: EAW86290.1.
CH471072 Genomic DNA. Translation: EAW86291.1.
CH471072 Genomic DNA. Translation: EAW86292.1.
CH471072 Genomic DNA. Translation: EAW86293.1.
BC000941 mRNA. Translation: AAH00941.1.
BC063816 mRNA. Translation: AAH63816.1.
CCDSCCDS55702.1. [P49903-3]
CCDS55703.1. [P49903-2]
CCDS7098.1. [P49903-1]
RefSeqNP_001182531.1. NM_001195602.1. [P49903-3]
NP_001182533.1. NM_001195604.1. [P49903-2]
NP_036379.2. NM_012247.4. [P49903-1]
UniGeneHs.124027.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3FD5X-ray1.90A/B1-392[»]
3FD6X-ray1.95A/B1-392[»]
ProteinModelPortalP49903.
SMRP49903. Positions 6-377.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116589. 23 interactions.
IntActP49903. 10 interactions.
STRING9606.ENSP00000367893.

PTM databases

PhosphoSiteP49903.

Polymorphism databases

DMDM27151792.

Proteomic databases

MaxQBP49903.
PaxDbP49903.
PeptideAtlasP49903.
PRIDEP49903.

Protocols and materials databases

DNASU22929.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000327347; ENSP00000367893; ENSG00000086475. [P49903-1]
ENST00000378614; ENSP00000367877; ENSG00000086475. [P49903-2]
ENST00000537130; ENSP00000442768; ENSG00000086475. [P49903-3]
ENST00000545675; ENSP00000441119; ENSG00000086475. [P49903-4]
GeneID22929.
KEGGhsa:22929.
UCSCuc001imh.3. human. [P49903-1]

Organism-specific databases

CTD22929.
GeneCardsGC10M013360.
HGNCHGNC:19685. SEPHS1.
HPAHPA037645.
MIM600902. gene.
neXtProtNX_P49903.
PharmGKBPA134905215.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0709.
HOGENOMHOG000219301.
HOVERGENHBG001207.
InParanoidP49903.
KOK01008.
OMADQKHLLC.
OrthoDBEOG7SR4MT.
PhylomeDBP49903.
TreeFamTF313811.

Enzyme and pathway databases

BRENDA2.7.9.3. 2681.

Gene expression databases

ArrayExpressP49903.
BgeeP49903.
CleanExHS_SEPHS1.
GenevestigatorP49903.

Family and domain databases

Gene3D3.30.1330.10. 1 hit.
3.90.650.10. 1 hit.
InterProIPR010918. AIR_synth_C_dom.
IPR000728. AIR_synth_N_dom.
IPR016188. PurM_N-like.
IPR004536. SelD.
[Graphical view]
PfamPF00586. AIRS. 1 hit.
PF02769. AIRS_C. 1 hit.
[Graphical view]
PIRSFPIRSF036407. Selenphspht_syn. 1 hit.
SUPFAMSSF55326. SSF55326. 1 hit.
SSF56042. SSF56042. 1 hit.
TIGRFAMsTIGR00476. selD. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP49903.
GeneWikiSelenophosphate_synthetase_1.
GenomeRNAi22929.
NextBio35492713.
PROP49903.
SOURCESearch...

Entry information

Entry nameSPS1_HUMAN
AccessionPrimary (citable) accession number: P49903
Secondary accession number(s): B4DWK0 expand/collapse secondary AC list , D3DRS9, D6PSQ9, Q5T5U8, Q5T5U9, Q9BVT4
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: December 13, 2002
Last modified: July 9, 2014
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 10

Human chromosome 10: entries, gene names and cross-references to MIM