P49903 (SPS1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	392 AA.
Sequence status	Complete.
Protein existence	Evidence 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.8
Subunit structure	Homodimer. Ref.8
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.

Ontologies

Keywords
Ligand	ATP-binding Nucleotide-binding Selenium
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cellular protein modification process Traceable author statement Ref.1. Source: ProtInc
Molecular_function	ATP binding Traceable author statement Ref.1. Source: ProtInc GTP binding Traceable author statement Ref.1. Source: ProtInc selenide, water dikinase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 392

392

Selenide, water dikinase 1

PRO_0000127648

Regions

Nucleotide binding

67 – 69

3

ATP

Nucleotide binding

162 – 164

3

ATP; shared with dimeric partner

Nucleotide binding

267 – 273

7

ATP

Sites

Active site

31

1

Potential

Binding site

32

1

ATP

Binding site

87

1

ATP

Binding site

110

1

ATP

Site

32

1

Important for catalytic activity By similarity

Experimental info

Mutagenesis

85

1

T → A: Strongly reduced ADP hydrolysis. Ref.8

Mutagenesis

268

1

G → C: No change in ATP-binding. Ref.1

Mutagenesis

270

1

G → R: No change in ATP-binding. Ref.1

Mutagenesis

273

1

G → A, D or V: Loss of ATP-binding. Ref.1

Mutagenesis

274

1

H → N: Reduced ATP-binding. Ref.1

Mutagenesis

274

1

H → Y: Increased ATP-binding. Ref.1

Sequence conflict

260

1

A → T in AAA87567. Ref.1

Sequence conflict

377 – 392

16

PQVAT…PGATS → HKWPLKT in AAA87567. Ref.1

Secondary structure

1

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392

Helix Strand Turn

Details...

Helix

10 – 12

3

Helix

20 – 23

4

Helix

35 – 42

8

Beta strand

68 – 74

7

Beta strand

81 – 89

9

Helix

96 – 113

18

Beta strand

120 – 129

10

Helix

134 – 154

21

Beta strand

159 – 169

11

Beta strand

171 – 180

10

Helix

182 – 184

3

Beta strand

196 – 201

6

Helix

205 – 213

9

Helix

230 – 245

16

Helix

249 – 257

9

Beta strand

262 – 265

4

Helix

270 – 279

10

Beta strand

283 – 296

14

Helix

299 – 305

7

Turn

306 – 308

3

Helix

312 – 314

3

Beta strand

324 – 328

5

Helix

330 – 341

12

Beta strand

352 – 362

11

Beta strand

364 – 375

12

Sequences

	Sequence		Length	Mass (Da)
	P49903 [UniParc]. Last modified December 13, 2002. Version 2. Checksum: E9636E38146D926D	FASTA	392	42,911
	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

References

	« Hide 'large scale' referencesShow '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], FUNCTION, ATP-BINDING, MUTAGENESIS OF GLY-268; GLY-270; GLY-273 AND HIS-274. Tissue: Liver.
[2]	"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. , 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].
[3]	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. , 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].
[4]	"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]. Tissue: Placenta and PNS.
[5]	Lubec G., Chen W.-Q., Sun Y. Submitted (DEC-2008) to UniProtKB Cited for: PROTEIN SEQUENCE OF 5-16 AND 64-76, MASS SPECTROMETRY. Tissue: Fetal brain cortex.
[6]	"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.
[7]	"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].
[8]	"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.
AL138764, AL355870 Genomic DNA. Translation: CAI12907.1.
AL355870, AL138764 Genomic DNA. Translation: CAI14198.1.
CH471072 Genomic DNA. Translation: EAW86290.1.
BC000941 mRNA. Translation: AAH00941.1.
BC063816 mRNA. Translation: AAH63816.1.

IPI

IPI00029056.

RefSeq

NP_036379.2. NM_012247.4.

UniGene

Hs.124027.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3FD5	X-ray	1.90	A/B	1-392	[»]
3FD6	X-ray	1.95	A/B	1-392	[»]

ProteinModelPortal

P49903.

ModBase

Search...

Protein-protein interaction databases

IntAct

P49903. 8 interactions.

STRING

9606.ENSP00000367893.

PTM databases

PhosphoSite

P49903.

Polymorphism databases

DMDM

27151792.

Proteomic databases

PaxDb

P49903.

PeptideAtlas

P49903.

PRIDE

P49903.

Protocols and materials databases

DNASU

22929.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000327347; ENSP00000367893; ENSG00000086475.

GeneID

22929.

KEGG

hsa:22929.

UCSC

uc001imh.3. human.

Organism-specific databases

CTD

22929.

GeneCards

GC10M013360.

HGNC

HGNC:19685. SEPHS1.

HPA

HPA037645.

MIM

600902. gene.

neXtProt

NX_P49903.

PharmGKB

PA134905215.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0709.

HOGENOM

HOG000219301.

HOVERGEN

HBG001207.

InParanoid

P49903.

KO

K01008.

OMA

PIRLTQY.

OrthoDB

EOG4ZW5B4.

Enzyme and pathway databases

BRENDA

2.7.9.3. 2681.

Gene expression databases

ArrayExpress

P49903.

Bgee

P49903.

CleanEx

HS_SEPHS1.

Genevestigator

P49903.

GermOnline

ENSG00000086475. Homo sapiens.

Family and domain databases

Gene3D

3.90.650.10. 1 hit.

InterPro

IPR010918. AIR_synth_C_dom.
IPR000728. AIR_synth_N_dom.
IPR016188. PurM_N-like.
IPR004536. SelD.
[Graphical view]

Pfam

PF00586. AIRS. 1 hit.
PF02769. AIRS_C. 1 hit.
[Graphical view]

PIRSF

PIRSF036407. Selenphspht_syn. 1 hit.

SUPFAM

SSF56042. AIR_synth_C. 1 hit.
SSF55326. PurM_N-like. 1 hit.

TIGRFAMs

TIGR00476. selD. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P49903.

GenomeRNAi

22929.

NextBio

43651.

SOURCE

Search...

Entry information

Entry name

SPS1_HUMAN

Accession

Primary (citable) accession number: P49903
Secondary accession number(s): Q5T5U8, Q9BVT4

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	December 13, 2002
Last modified:	May 29, 2013
This is version 113 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.