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Q9HD40 (SPCS_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 85. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | 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:
O-phosphoseryl-tRNA(Sec) selenium transferase

EC=2.9.1.2
Alternative name(s):
Liver-pancreas antigen
Short name=LP
SLA-p35
SLA/LP autoantigen
Selenocysteine synthase
Short name=Sec synthase
Selenocysteinyl-tRNA(Sec) synthase
Sep-tRNA:Sec-tRNA synthase
Short name=SepSecS
Soluble liver antigen
Short name=SLA
UGA suppressor tRNA-associated protein
tRNA(Ser/Sec)-associated antigenic protein
Gene names
Name:SEPSECS
Synonyms:TRNP48
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length501 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis. Ref.11

Catalytic activity

O-phospho-L-seryl-tRNA(Sec) + selenophosphate = L-selenocysteinyl-tRNA(Sec) + phosphate.

Cofactor

Pyridoxal phosphate. Ref.11

Pathway

Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; selenocysteinyl-tRNA(Sec) from L-seryl-tRNA(Sec) (archaeal/eukaryal route): step 2/2.

Subcellular location

Cytoplasm.

Tissue specificity

Primarily expressed in liver, pancreas, kidney and lung. Overexpressed in PHA-stimulated T-cells.

Involvement in disease

Defects in SEPSECS are the cause of pontocerebellar hypoplasia type 2D (PCH2D) [MIM:613811]. PCH2D is a disorder characterized by postnatal onset of progressive atrophy of the cerebrum and cerebellum, microcephaly, profound mental retardation, spasticity, and variable seizures. Ref.13

Miscellaneous

Possible diagnostic marker for autoimmune hepatitis (AIH).

Sequence similarities

Belongs to the SepSecS family.

Sequence caution

The sequence AAD33963.2 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.

The sequence AAH23539.1 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.

The sequence CAB62209.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

The sequence CAB89517.1 differs from that shown. Reason: Frameshift at position 39.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9HD40-1)

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: Q9HD40-2)

The sequence of this isoform differs from the canonical sequence as follows:
     39-47: GKCPENGWD → VHSWHWTIR
     48-501: Missing.
Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available.
Isoform 3 (identifier: Q9HD40-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-38: MNRESFAAGERLVSPAYVRQGCEARRSHEHLIRLLLEK → MQCDDLGSLQPPPPGFTPFACLSLPSSWDYRRPPPHP

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 501501O-phosphoseryl-tRNA(Sec) selenium transferase
PRO_0000219875

Regions

Region474 – 49320SLA/LP epitope

Amino acid modifications

Modified residue2841N6-(pyridoxal phosphate)lysine
Modified residue5011Phosphoserine Ref.12

Natural variations

Alternative sequence1 – 3838MNRES…LLLEK → MQCDDLGSLQPPPPGFTPFA CLSLPSSWDYRRPPPHP in isoform 3.
VSP_038080
Alternative sequence39 – 479GKCPENGWD → VHSWHWTIR in isoform 2.
VSP_038078
Alternative sequence48 – 501454Missing in isoform 2.
VSP_038079
Natural variant2391A → T in PCH2D; abrogates enzyme activity. Ref.13
VAR_065585
Natural variant3341Y → C in PCH2D; abrogates enzyme activity. Ref.13
VAR_065586

Experimental info

Mutagenesis2841K → A: Loss of activity. Ref.11
Sequence conflict981S → P in AAG00491. Ref.8
Sequence conflict2641H → R in BAF85165. Ref.1
Sequence conflict3981R → K in AAD33963. Ref.6
Sequence conflict3981R → K in CAB89517. Ref.6
Sequence conflict4521K → N in AAD33963. Ref.6
Sequence conflict4521K → N in CAB89517. Ref.6
Sequence conflict4671K → R in AAG00491. Ref.8

Secondary structure

............................................................... 501
Helix Strand Turn

Details...

Sequences

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

Last modified March 29, 2005. Version 2.
Checksum: 7136FB390B18760B

FASTA50155,726
        10         20         30         40         50         60 
MNRESFAAGE RLVSPAYVRQ GCEARRSHEH LIRLLLEKGK CPENGWDEST LELFLHELAI 

        70         80         90        100        110        120 
MDSNNFLGNC GVGEREGRVA SALVARRHYR FIHGIGRSGD ISAVQPKAAG SSLLNKITNS 

       130        140        150        160        170        180 
LVLDIIKLAG VHTVANCFVV PMATGMSLTL CFLTLRHKRP KAKYIIWPRI DQKSCFKSMI 

       190        200        210        220        230        240 
TAGFEPVVIE NVLEGDELRT DLKAVEAKVQ ELGPDCILCI HSTTSCFAPR VPDRLEELAV 

       250        260        270        280        290        300 
ICANYDIPHI VNNAYGVQSS KCMHLIQQGA RVGRIDAFVQ SLDKNFMVPV GGAIIAGFND 

       310        320        330        340        350        360 
SFIQEISKMY PGRASASPSL DVLITLLSLG SNGYKKLLKE RKEMFSYLSN QIKKLSEAYN 

       370        380        390        400        410        420 
ERLLHTPHNP ISLAMTLKTL DEHRDKAVTQ LGSMLFTRQV SGARVVPLGS MQTVSGYTFR 

       430        440        450        460        470        480 
GFMSHTNNYP CAYLNAASAI GMKMQDVDLF IKRLDRCLKA VRKERSKESD DNYDKTEDVD 

       490        500 
IEEMALKLDN VLLDTYQDAS S 

« Hide

Isoform 2 [UniParc].

Checksum: 958F3F91D272149B
Show »

FASTA475,627
Isoform 3 [UniParc].

Checksum: 82AE23050D9C2011
Show »

FASTA50055,411

References

« Hide 'large scale' references
[1]"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: 14702039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Testis.
[2]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Endometrium.
[3]"Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. expand/collapse author list , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
Nature 434:724-731(2005) [PubMed: 15815621] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]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 (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3).
Tissue: Brain and Muscle.
[6]"Identification of target antigen for SLA/LP autoantibodies in autoimmune hepatitis."
Wies I., Brunner S., Henninger J., Herkel J., Kanzler S., Meyer zum Bueschenfelde K.-H., Lohse A.W.
Lancet 355:1510-1515(2000) [PubMed: 10801173] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 29-501 (ISOFORM 1), NUCLEOTIDE SEQUENCE [MRNA] OF 29-501 (ISOFORM 2).
Tissue: Liver and T-cell lymphoma.
[7]"Isolation and characterization of cDNA encoding the antigenic protein of the human tRNP(Ser)Sec complex recognized by autoantibodies from patients withtype-1 autoimmune hepatitis."
Costa M., Rodriguez-Sanchez J.L., Czaja A.J., Gelpi C.
Clin. Exp. Immunol. 121:364-374(2000) [PubMed: 10931155] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 61-501 (ISOFORM 1).
Tissue: Liver.
[8]"Coding sequence of the human SLA/LP autoantigen."
Seelig H.-P., Wiemann C., Plaikner M., Schranz P., Seelig R., Renz M.
Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 61-501 (ISOFORM 1).
Tissue: Liver.
[9]"Soluble liver antigen: isolation of a 35-kd recombinant protein (SLA-p35) specifically recognizing sera from patients with autoimmune hepatitis."
Volkmann M., Martin L., Baeurle A., Heid H., Strassburg C.P., Trautwein C., Fiehn W., Manns M.P.
Hepatology 33:591-596(2001) [PubMed: 11230739] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 208-501.
[10]"Fine specificity of autoantibodies to soluble liver antigen and liver/pancreas."
Herkel J., Heidrich B., Nieraad N., Wies I., Rother M., Lohse A.W.
Hepatology 35:403-408(2002) [PubMed: 11826415] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 434-493, SLA/LP EPITOPE MAPPING.
[11]"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: 17142313] [Abstract]
Cited for: FUNCTION, COFACTOR, MUTAGENESIS OF LYS-284.
[12]"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: 19413330] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-501, MASS SPECTROMETRY.
Tissue: Embryonic kidney.
[13]"Mutations disrupting selenocysteine formation cause progressive cerebello-cerebral atrophy."
Agamy O., Ben Zeev B., Lev D., Marcus B., Fine D., Su D., Narkis G., Ofir R., Hoffmann C., Leshinsky-Silver E., Flusser H., Sivan S., Soll D., Lerman-Sagie T., Birk O.S.
Am. J. Hum. Genet. 87:538-544(2010) [PubMed: 20920667] [Abstract]
Cited for: VARIANTS PCH2D THR-239 AND CYS-334, CHARACTERIZATION OF VARIANTS PCH2D THR-239 AND CYS-334.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK292476 mRNA. Translation: BAF85165.1.
BX648976 mRNA. No translation available.
AC007073 Genomic DNA. No translation available.
AC104662 Genomic DNA. No translation available.
CH471069 Genomic DNA. Translation: EAW92832.1.
BC023539 mRNA. Translation: AAH23539.1. Sequence problems.
BC117202 mRNA. Translation: AAI17203.1.
AF146396 mRNA. Translation: AAD33963.2. Sequence problems.
AJ277541 mRNA. Translation: CAB89517.1. Frameshift.
AJ238617 mRNA. Translation: CAB62209.1. Different initiation.
AF282065 mRNA. Translation: AAG00491.1.
IPIIPI00155389.
IPI00302283.
IPI00930339.
RefSeqNP_058651.3. NM_016955.3.
UniGeneHs.253305.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3HL2X-ray2.81A/B/C/D1-501[»]
ProteinModelPortalQ9HD40.
SMRQ9HD40. Positions 20-464.
ModBaseSearch...

Protein-protein interaction databases

STRINGQ9HD40.

PTM databases

PhosphoSiteQ9HD40.

Polymorphism databases

DMDM62287911.

Proteomic databases

PRIDEQ9HD40.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000358971; ENSP00000351857; ENSG00000109618.
ENST00000382103; ENSP00000371535; ENSG00000109618.
GeneID51091.
KEGGhsa:51091.
UCSCuc003grh.1. human.

Organism-specific databases

CTD51091.
GeneCardsGC04M025121.
H-InvDBHIX0024557.
HGNCHGNC:30605. SEPSECS.
MIM613009. gene.
613811. phenotype.
neXtProtNX_Q9HD40.
Orphanet2524. Pontocerebellar hypoplasia type 2.
247198. Progressive cerebello-cerebral atrophy.
PharmGKBPA162402915.
GenAtlasSearch...

Phylogenomic databases

GeneTreeENSGT00390000007332.
HOGENOMHBG716333.
HOVERGENHBG061363.
InParanoidQ9HD40.
OMAIPHVVNN.
OrthoDBEOG4JQ3XB.
PhylomeDBQ9HD40.

Gene expression databases

ArrayExpressQ9HD40.
BgeeQ9HD40.
CleanExHS_SEPSECS.
GenevestigatorQ9HD40.
GermOnlineENSG00000109618. Homo sapiens.

Family and domain databases

InterProIPR019793. Peroxidases_heam-ligand_BS.
IPR015424. PyrdxlP-dep_Trfase_major_dom.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR019872. Sec-tRNA_Se_transferase.
IPR008829. SLA/LP_auto_ag.
[Graphical view]
Gene3DG3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.
KOK03341.
PANTHERPTHR12944. Sec-tRNA_Se_transferase. 1 hit.
PfamPF05889. SLA_LP_auto_ag. 1 hit.
[Graphical view]
SUPFAMSSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
TIGRFAMsTIGR03531. Selenium_SpcS. 1 hit.
ProtoNetSearch...

Other

DrugBankDB00114. Pyridoxal Phosphate.
NextBio53771.
SOURCESearch...

Entry information

Entry nameSPCS_HUMAN
AccessionPrimary (citable) accession number: Q9HD40
Secondary accession number(s): A8K8W1 expand/collapse secondary AC list , Q0D2P3, Q17RT1, Q9NXZ5, Q9UGM9, Q9Y353
Entry history
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: March 29, 2005
Last modified: January 25, 2012
This is version 85 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

Human chromosome 4

Human chromosome 4: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families