Q6P6M7 (SPCS_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
O-phosphoseryl-tRNA(Sec) selenium transferase
EC=2.9.1.2

Alternative name(s):
Selenocysteine synthase
Short name=Sec synthase
Selenocysteinyl-tRNA(Sec) synthase
Sep-tRNA:Sec-tRNA synthase
Short name=SepSecS
UGA suppressor tRNA-associated protein

Gene names

Name:	Sepsecs
Synonyms:	D5Ertd135e

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	504 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis By similarity.
Catalytic activity	O-phospho-L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + phosphate.
Cofactor	Pyridoxal phosphate. Ref.3
Pathway	Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; selenocysteinyl-tRNA(Sec) from L-seryl-tRNA(Sec) (archaeal/eukaryal route): step 2/2.
Subunit structure	Homotetramer formed by a catalytic dimer and a non-catalytic dimer serving as a binding platform that orients tRNASec for catalysis. Ref.3
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the SepSecS family.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate RNA-binding Selenium tRNA-binding
Molecular function	Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	selenocysteine incorporation Inferred from direct assay PubMed 16230358. Source: HGNC selenocysteinyl-tRNA(Sec) biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	cytoplasm Inferred from direct assay PubMed 16230358. Source: HGNC nucleus Inferred from direct assay PubMed 16230358. Source: HGNC
Molecular_function	pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro tRNA binding Inferred from direct assay PubMed 16230358. Source: HGNC transferase activity, transferring selenium-containing groups Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 504

504

O-phosphoseryl-tRNA(Sec) selenium transferase

PRO_0000219876

Regions

Region

1 – 44

44

Tetramerization

Region

96 – 106

11

Phosphate loop (P-loop)

Sites

Binding site

75

1

PLP

Binding site

97

1

Substrate

Binding site

98

1

Substrate

Binding site

105

1

Substrate

Binding site

271

1

tRNA variable arm By similarity

Binding site

313

1

Substrate

Binding site

398

1

tRNA discriminator base By similarity

Site

74

1

May act as a substrate filter by repelling compounds with a negatively charged alpha-carboxylate

Amino acid modifications

Modified residue

284

1

N6-(pyridoxal phosphate)lysine

Experimental info

Mutagenesis

105

1

Q → E: 50% of wild-type activity. Ref.3

Mutagenesis

313

1

R → E: Virtually inactive. Ref.3

Mutagenesis

313

1

R → S: 30% of wild-type activity. Ref.3

Sequence conflict

300

1

E → D in AAH62133. Ref.2

Secondary structure

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504

Helix Strand Turn

Details...

Helix

24 – 38

15

Helix

48 – 60

13

Helix

63 – 65

3

Helix

82 – 87

6

Turn

88 – 90

3

Beta strand

95 – 97

3

Helix

109 – 129

21

Beta strand

136 – 142

7

Helix

144 – 158

15

Beta strand

164 – 168

5

Helix

173 – 181

9

Beta strand

185 – 189

5

Beta strand

192 – 194

3

Beta strand

197 – 199

3

Helix

202 – 212

11

Helix

214 – 216

3

Beta strand

217 – 225

9

Helix

235 – 245

11

Beta strand

249 – 252

4

Turn

254 – 258

5

Helix

260 – 272

13

Beta strand

277 – 281

5

Helix

282 – 286

5

Beta strand

293 – 298

6

Helix

300 – 309

10

Helix

317 – 358

42

Beta strand

370 – 376

7

Turn

378 – 380

3

Beta strand

381 – 385

5

Helix

387 – 397

11

Beta strand

404 – 406

3

Beta strand

411 – 414

4

Beta strand

417 – 420

4

Turn

421 – 425

5

Beta strand

433 – 437

5

Helix

444 – 465

22

Sequences

	Sequence		Length	Mass (Da)
	Q6P6M7 [UniParc]. Last modified March 29, 2005. Version 2. Checksum: E106674A0C80D98B	FASTA	504	55,326
	10 20 30 40 50 60 MNPESFAAGE RRVSPAYVRQ GCEARRAHEH LIRLLLEQGK CPEDGWDEST LELFLHELAV 70 80 90 100 110 120 MDSNNFLGNC GVGEREGRVA SALVARRHYR FIHGIGRSGD ISAVQPKAAG SSLLNKITNS 130 140 150 160 170 180 LVLNVIKLAG VHSVASCFVV PMATGMSLTL CFLTLRHKRP KAKYIIWPRI DQKSCFKSMV 190 200 210 220 230 240 TAGFEPVVIE NVLEGDELRT DLKAVEAKIQ ELGPEHILCL HSTTACFAPR VPDRLEELAV 250 260 270 280 290 300 ICANYDIPHV VNNAYGLQSS KCMHLIQQGA RVGRIDAFVQ SLDKNFMVPV GGAIIAGFNE 310 320 330 340 350 360 PFIQDISKMY PGRASASPSL DVLITLLSLG CSGYRKLLKE RKEMFVYLST QLKKLAEAHN 370 380 390 400 410 420 ERLLQTPHNP ISLAMTLKTI DGHHDKAVTQ LGSMLFTRQV SGARAVPLGN VQTVSGHTFR 430 440 450 460 470 480 GFMSHADNYP CAYLNAAAAI GMKMQDVDLF IKRLDKCLNI VRKEQTRASV VSGADRNKAE 490 500 DADIEEMALK LDDVLGDVGQ GPAL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: C57BL/6J. Tissue: Cecum.
[2]	"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: Limb.
[3]	"Structure and catalytic mechanism of eukaryotic selenocysteine synthase." Ganichkin O.M., Xu X.M., Carlson B.A., Mix H., Hatfield D.L., Gladyshev V.N., Wahl M.C. J. Biol. Chem. 283:5849-5865(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 19-468 IN COMPLEX WITH PYRIDOXAL PHOSPHATE, SUBUNIT, SUBSTRATE-BINDING SITES, COFACTOR, MUTAGENESIS OF GLN-105 AND ARG-313.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AK033654 mRNA. Translation: BAC28410.1.
BC062133 mRNA. Translation: AAH62133.1.

IPI

IPI00227678.

RefSeq

NP_766078.1. NM_172490.3.

UniGene

Mm.244719.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3BC8	X-ray	1.65	A	19-468	[»]
3BCA	X-ray	2.25	A	19-468	[»]
3BCB	X-ray	1.85	A	19-468	[»]

ProteinModelPortal

Q6P6M7.

SMR

Q6P6M7. Positions 23-467.

ModBase

Search...

Protein-protein interaction databases

STRING

10090.ENSMUSP00000031069.

PTM databases

PhosphoSite

Q6P6M7.

Proteomic databases

PaxDb

Q6P6M7.

PRIDE

Q6P6M7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000031069; ENSMUSP00000031069; ENSMUSG00000029173.

GeneID

211006.

KEGG

mmu:211006.

UCSC

uc008xko.1. mouse.

Organism-specific databases

CTD

51091.

MGI

MGI:1098791. Sepsecs.

Phylogenomic databases

eggNOG

COG0076.

GeneTree

ENSGT00390000007332.

HOGENOM

HOG000254245.

HOVERGEN

HBG061363.

InParanoid

Q6P6M7.

KO

K03341.

OMA

IPHVVNN.

OrthoDB

EOG4JQ3XB.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-14964.

UniPathway

UPA00906; UER00898.

Gene expression databases

ArrayExpress

Q6P6M7.

Bgee

Q6P6M7.

Genevestigator

Q6P6M7.

GermOnline

ENSMUSG00000029173. Mus musculus.

Family and domain databases

Gene3D

3.40.640.10. 1 hit.

InterPro

IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR019872. Sec-tRNA_Se_transferase.
IPR008829. SLA/LP_auto_ag.
[Graphical view]

PANTHER

PTHR12944. PTHR12944. 1 hit.

Pfam

PF05889. SLA_LP_auto_ag. 1 hit.
[Graphical view]

PIRSF

PIRSF017689. SepSecS. 1 hit.

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

TIGRFAMs

TIGR03531. selenium_SpcS. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q6P6M7.

NextBio

373121.

SOURCE

Search...

Entry information

Entry name

SPCS_MOUSE

Accession

Primary (citable) accession number: Q6P6M7
Secondary accession number(s): Q8BZS6

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	March 29, 2005
Last modified:	April 3, 2013
This is version 75 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program