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P51160

- PDE6C_HUMAN

UniProt

P51160 - PDE6C_HUMAN

Protein

Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'

Gene

PDE6C

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 136 (01 Oct 2014)
      Sequence version 2 (07 Mar 2006)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.

    Cofactori

    Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions, while site 2 has a preference for magnesium and/or manganese ions By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei97 – 971cGMPBy similarity
    Binding sitei116 – 1161cGMPBy similarity
    Binding sitei176 – 1761cGMPBy similarity
    Active sitei562 – 5621Proton donorBy similarity
    Metal bindingi566 – 5661Divalent metal cation 1By similarity
    Metal bindingi602 – 6021Divalent metal cation 1By similarity
    Metal bindingi603 – 6031Divalent metal cation 1By similarity
    Metal bindingi603 – 6031Divalent metal cation 2By similarity
    Metal bindingi723 – 7231Divalent metal cation 1By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi169 – 1724cGMPBy similarity

    GO - Molecular functioni

    1. 3',5'-cyclic-GMP phosphodiesterase activity Source: UniProtKB-EC
    2. cGMP binding Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. phototransduction, visible light Source: Ensembl
    2. retinal cone cell development Source: Ensembl
    3. visual perception Source: ProtInc

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Sensory transduction, Vision

    Keywords - Ligandi

    cGMP, cGMP-binding, Metal-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' (EC:3.1.4.35)
    Alternative name(s):
    cGMP phosphodiesterase 6C
    Gene namesi
    Name:PDE6C
    Synonyms:PDEA2
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 10

    Organism-specific databases

    HGNCiHGNC:8787. PDE6C.

    Subcellular locationi

    Cell membrane Curated; Lipid-anchor Curated; Cytoplasmic side Curated

    GO - Cellular componenti

    1. plasma membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Cone dystrophy 4 (COD4) [MIM:613093]: An early-onset cone dystrophy. Cone dystrophies are retinal dystrophies characterized by progressive degeneration of the cone photoreceptors with preservation of rod function, as indicated by electroretinogram. However, some rod involvement may be present in some cone dystrophies, particularly at late stage. Affected individuals suffer from photophobia, loss of visual acuity, color vision and central visual field. Another sign is the absence of macular lesions for many years. Cone dystrophies are distinguished from the cone-rod dystrophies in which some loss of peripheral vision also occurs.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti29 – 291R → W in COD4. 1 Publication
    VAR_062408
    Natural varianti323 – 3231Y → N in COD4. 1 Publication
    VAR_062409
    Natural varianti455 – 4551M → V in COD4. 1 Publication
    VAR_062410

    Keywords - Diseasei

    Disease mutation

    Organism-specific databases

    MIMi613093. phenotype.
    Orphaneti49382. Achromatopsia.
    1871. Progressive cone dystrophy.
    PharmGKBiPA33135.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 855855Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'PRO_0000198831Add
    BLAST
    Propeptidei856 – 8583Removed in mature formSequence AnalysisPRO_0000370788

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei855 – 8551Cysteine methyl esterSequence Analysis
    Lipidationi855 – 8551S-geranylgeranyl cysteineBy similarity

    Keywords - PTMi

    Lipoprotein, Methylation, Prenylation

    Proteomic databases

    PaxDbiP51160.
    PRIDEiP51160.

    PTM databases

    PhosphoSiteiP51160.

    Expressioni

    Gene expression databases

    BgeeiP51160.
    CleanExiHS_PDE6C.
    GenevestigatoriP51160.

    Interactioni

    Subunit structurei

    Composed of two alpha' subunits that are associated with 3 smaller proteins of 11, 13, and 15 kDa.

    Protein-protein interaction databases

    STRINGi9606.ENSP00000360502.

    Structurei

    Secondary structure

    1
    858
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi746 – 7549
    Helixi762 – 7643
    Helixi766 – 7716
    Helixi772 – 78211

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3JWQX-ray2.87A/B/C/D746-785[»]
    3JWRX-ray2.99A/B746-785[»]
    ProteinModelPortaliP51160.
    SMRiP51160. Positions 24-820.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini75 – 224150GAF 1Add
    BLAST
    Domaini256 – 433178GAF 2Add
    BLAST

    Sequence similaritiesi

    Contains 2 GAF domains.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiNOG290744.
    HOGENOMiHOG000007069.
    HOVERGENiHBG053539.
    InParanoidiP51160.
    KOiK13757.
    OMAiCGIRLFF.
    OrthoDBiEOG7BGHK1.
    PhylomeDBiP51160.
    TreeFamiTF316499.

    Family and domain databases

    Gene3Di1.10.1300.10. 1 hit.
    3.30.450.40. 3 hits.
    InterProiIPR003018. GAF.
    IPR029016. GAF_dom_like.
    IPR003607. HD/PDEase_dom.
    IPR023088. PDEase.
    IPR002073. PDEase_catalytic_dom.
    IPR023174. PDEase_CS.
    [Graphical view]
    PfamiPF01590. GAF. 2 hits.
    PF00233. PDEase_I. 1 hit.
    [Graphical view]
    PRINTSiPR00387. PDIESTERASE1.
    SMARTiSM00065. GAF. 2 hits.
    SM00471. HDc. 1 hit.
    [Graphical view]
    SUPFAMiSSF55781. SSF55781. 3 hits.
    PROSITEiPS00126. PDEASE_I. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P51160-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGEINQVAVE KYLEENPQFA KEYFDRKLRV EVLGEIFKNS QVPVQSSMSF    50
    SELTQVEESA LCLELLWTVQ EEGGTPEQGV HRALQRLAHL LQADRCSMFL 100
    CRSRNGIPEV ASRLLDVTPT SKFEDNLVGP DKEVVFPLDI GIVGWAAHTK 150
    KTHNVPDVKK NSHFSDFMDK QTGYVTKNLL ATPIVVGKEV LAVIMAVNKV 200
    NASEFSKQDE EVFSKYLNFV SIILRLHHTS YMYNIESRRS QILMWSANKV 250
    FEELTDVERQ FHKALYTVRS YLNCERYSIG LLDMTKEKEF YDEWPIKLGE 300
    VEPYKGPKTP DGREVNFYKI IDYILHGKEE IKVIPTPPAD HWTLISGLPT 350
    YVAENGFICN MMNAPADEYF TFQKGPVDET GWVIKNVLSL PIVNKKEDIV 400
    GVATFYNRKD GKPFDEHDEY ITETLTQFLG WSLLNTDTYD KMNKLENRKD 450
    IAQEMLMNQT KATPEEIKSI LKFQEKLNVD VIDDCEEKQL VAILKEDLPD 500
    PRSAELYEFR FSDFPLTEHG LIKCGIRLFF EINVVEKFKV PVEVLTRWMY 550
    TVRKGYRAVT YHNWRHGFNV GQTMFTLLMT GRLKKYYTDL EAFAMLAAAF 600
    CHDIDHRGTN NLYQMKSTSP LARLHGSSIL ERHHLEYSKT LLQDESLNIF 650
    QNLNKRQFET VIHLFEVAII ATDLALYFKK RTMFQKIVDA CEQMQTEEEA 700
    IKYVTVDPTK KEIIMAMMMT ACDLSAITKP WEVQSQVALM VANEFWEQGD 750
    LERTVLQQQP IPMMDRNKRD ELPKLQVGFI DFVCTFVYKE FSRFHKEITP 800
    MLSGLQNNRV EWKSLADEYD AKMKVIEEEA KKQEGGAEKA AEDSGGGDDK 850
    KSKTCLML 858
    Length:858
    Mass (Da):99,147
    Last modified:March 7, 2006 - v2
    Checksum:i06FFD025EE5936A5
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti116 – 1161D → V in AAA96392. (PubMed:8543163)Curated
    Sequence conflicti116 – 1161D → V in AAA92886. (PubMed:7490077)Curated
    Sequence conflicti373 – 3731Q → P in AAA96392. (PubMed:8543163)Curated
    Sequence conflicti464 – 4641P → L in AAA96392. (PubMed:8543163)Curated
    Sequence conflicti565 – 5651R → Q in AAA96392. (PubMed:8543163)Curated
    Sequence conflicti565 – 5651R → Q in AAA92886. (PubMed:7490077)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti29 – 291R → W in COD4. 1 Publication
    VAR_062408
    Natural varianti157 – 1571D → E Rare polymorphism. 1 Publication
    Corresponds to variant rs76999928 [ dbSNP | Ensembl ].
    VAR_025470
    Natural varianti270 – 2701S → T.1 Publication
    Corresponds to variant rs701865 [ dbSNP | Ensembl ].
    VAR_050475
    Natural varianti323 – 3231Y → N in COD4. 1 Publication
    VAR_062409
    Natural varianti455 – 4551M → V in COD4. 1 Publication
    VAR_062410
    Natural varianti699 – 6991E → A.
    Corresponds to variant rs12261131 [ dbSNP | Ensembl ].
    VAR_050476
    Natural varianti822 – 8221K → N Rare polymorphism. 1 Publication
    Corresponds to variant rs79487435 [ dbSNP | Ensembl ].
    VAR_025471
    Natural varianti826 – 8261I → S Found in a renal cell carcinoma sample; somatic mutation. 1 Publication
    VAR_064744
    Natural varianti834 – 8341E → G Rare polymorphism. 1 Publication
    VAR_025472

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U31973 mRNA. Translation: AAA96392.1.
    U20212
    , U20196, U20197, U20199, U20200, U20201, U20202, U20203, U20204, U20205, U20206, U20207, U20208, U20209, U20210, U20211 Genomic DNA. Translation: AAA92886.1.
    X94354 Genomic DNA. Translation: CAA64079.1.
    AL356214, AL157396 Genomic DNA. Translation: CAH72330.1.
    AL157396, AL356214 Genomic DNA. Translation: CAH73839.1.
    CH471066 Genomic DNA. Translation: EAW50064.1.
    CCDSiCCDS7429.1.
    PIRiS63688. JC4520.
    RefSeqiNP_006195.3. NM_006204.3.
    UniGeneiHs.658121.

    Genome annotation databases

    EnsembliENST00000371447; ENSP00000360502; ENSG00000095464.
    GeneIDi5146.
    KEGGihsa:5146.
    UCSCiuc001kiu.4. human.

    Polymorphism databases

    DMDMi90111861.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U31973 mRNA. Translation: AAA96392.1 .
    U20212
    , U20196 , U20197 , U20199 , U20200 , U20201 , U20202 , U20203 , U20204 , U20205 , U20206 , U20207 , U20208 , U20209 , U20210 , U20211 Genomic DNA. Translation: AAA92886.1 .
    X94354 Genomic DNA. Translation: CAA64079.1 .
    AL356214 , AL157396 Genomic DNA. Translation: CAH72330.1 .
    AL157396 , AL356214 Genomic DNA. Translation: CAH73839.1 .
    CH471066 Genomic DNA. Translation: EAW50064.1 .
    CCDSi CCDS7429.1.
    PIRi S63688. JC4520.
    RefSeqi NP_006195.3. NM_006204.3.
    UniGenei Hs.658121.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3JWQ X-ray 2.87 A/B/C/D 746-785 [» ]
    3JWR X-ray 2.99 A/B 746-785 [» ]
    ProteinModelPortali P51160.
    SMRi P51160. Positions 24-820.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 9606.ENSP00000360502.

    Chemistry

    BindingDBi P51160.
    ChEMBLi CHEMBL2363066.

    PTM databases

    PhosphoSitei P51160.

    Polymorphism databases

    DMDMi 90111861.

    Proteomic databases

    PaxDbi P51160.
    PRIDEi P51160.

    Protocols and materials databases

    DNASUi 5146.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000371447 ; ENSP00000360502 ; ENSG00000095464 .
    GeneIDi 5146.
    KEGGi hsa:5146.
    UCSCi uc001kiu.4. human.

    Organism-specific databases

    CTDi 5146.
    GeneCardsi GC10P095362.
    GeneReviewsi PDE6C.
    H-InvDB HIX0035433.
    HGNCi HGNC:8787. PDE6C.
    MIMi 600827. gene.
    613093. phenotype.
    neXtProti NX_P51160.
    Orphaneti 49382. Achromatopsia.
    1871. Progressive cone dystrophy.
    PharmGKBi PA33135.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG290744.
    HOGENOMi HOG000007069.
    HOVERGENi HBG053539.
    InParanoidi P51160.
    KOi K13757.
    OMAi CGIRLFF.
    OrthoDBi EOG7BGHK1.
    PhylomeDBi P51160.
    TreeFami TF316499.

    Miscellaneous databases

    GeneWikii PDE6C.
    GenomeRNAii 5146.
    NextBioi 19856.
    PROi P51160.
    SOURCEi Search...

    Gene expression databases

    Bgeei P51160.
    CleanExi HS_PDE6C.
    Genevestigatori P51160.

    Family and domain databases

    Gene3Di 1.10.1300.10. 1 hit.
    3.30.450.40. 3 hits.
    InterProi IPR003018. GAF.
    IPR029016. GAF_dom_like.
    IPR003607. HD/PDEase_dom.
    IPR023088. PDEase.
    IPR002073. PDEase_catalytic_dom.
    IPR023174. PDEase_CS.
    [Graphical view ]
    Pfami PF01590. GAF. 2 hits.
    PF00233. PDEase_I. 1 hit.
    [Graphical view ]
    PRINTSi PR00387. PDIESTERASE1.
    SMARTi SM00065. GAF. 2 hits.
    SM00471. HDc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55781. SSF55781. 3 hits.
    PROSITEi PS00126. PDEASE_I. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation and characterization of a cDNA encoding the alpha' subunit of human cone cGMP-phosphodiesterase."
      Viczian A.S., Piriev N.I., Farber D.B.
      Gene 166:205-211(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Tissue: Retina.
    2. "Gene structure and amino acid sequence of the human cone photoreceptor cGMP-phosphodiesterase alpha' subunit (PDEA2) and its chromosomal localization to 10q24."
      Piriev N.I., Viczian A.S., Ye J., Kerner B., Korenberg J.R., Farber D.B.
      Genomics 28:429-435(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Tissue: Retina.
    3. "Human cone-specific cGMP phosphodiesterase alpha' subunit: complete cDNA sequence and gene arrangement."
      Feshchenko E.A., Andreeva S.G., Suslova V.A., Smirnova E.V., Zagranichny V.E., Lipkin V.M.
      FEBS Lett. 381:149-152(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], VARIANT THR-270.
      Tissue: Retina.
    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.
      , 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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "Screening of the gene encoding the alpha'-subunit of cone cGMP-PDE in patients with retinal degenerations."
      Gao Y.Q., Danciger M., Longmuir R., Piriev N.I., Zhao D.Y., Heckenlively J.R., Fishman G.A., Weleber R.G., Jacobson S.G., Stone E.M., Farber D.B.
      Invest. Ophthalmol. Vis. Sci. 40:1818-1822(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS GLU-157; ASN-822 AND GLY-834.
    7. Cited for: VARIANTS COD4 TRP-29; ASN-323 AND VAL-455.
    8. Cited for: VARIANT SER-826.

    Entry informationi

    Entry nameiPDE6C_HUMAN
    AccessioniPrimary (citable) accession number: P51160
    Secondary accession number(s): A6NCR6, Q5VY29
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: March 7, 2006
    Last modified: October 1, 2014
    This is version 136 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (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.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 10
      Human chromosome 10: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3