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P16499

- PDE6A_HUMAN

UniProt

P16499 - PDE6A_HUMAN

Protein

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

Gene

PDE6A

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 145 (01 Oct 2014)
      Sequence version 4 (25 Nov 2008)
      Previous versions | rss
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    Functioni

    This protein participates in processes of transmission and amplification of the visual signal.

    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
    Active sitei559 – 5591Proton donorBy similarity
    Metal bindingi563 – 5631Divalent metal cation 1By similarity
    Metal bindingi599 – 5991Divalent metal cation 1By similarity
    Metal bindingi600 – 6001Divalent metal cation 1By similarity
    Metal bindingi600 – 6001Divalent metal cation 2By similarity
    Metal bindingi720 – 7201Divalent metal cation 1By similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. cytosolic calcium ion homeostasis Source: BHF-UCL
    2. GMP metabolic process Source: BHF-UCL
    3. phototransduction, visible light Source: Reactome
    4. regulation of rhodopsin mediated signaling pathway Source: Reactome
    5. retina development in camera-type eye Source: Ensembl
    6. rhodopsin mediated signaling pathway Source: Reactome
    7. visual perception Source: ProtInc

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Sensory transduction, Vision

    Keywords - Ligandi

    cGMP, Metal-binding

    Enzyme and pathway databases

    ReactomeiREACT_163919. Inactivation, recovery and regulation of the phototransduction cascade.
    REACT_163932. Activation of the phototransduction cascade.
    REACT_172761. Ca2+ pathway.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (EC:3.1.4.35)
    Short name:
    GMP-PDE alpha
    Alternative name(s):
    PDE V-B1
    Gene namesi
    Name:PDE6A
    Synonyms:PDEA
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 5

    Organism-specific databases

    HGNCiHGNC:8785. PDE6A.

    Subcellular locationi

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

    GO - Cellular componenti

    1. photoreceptor disc membrane Source: Reactome
    2. plasma membrane Source: Reactome

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Retinitis pigmentosa 43 (RP43) [MIM:613810]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.2 Publications
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti102 – 1021R → H in RP43. 1 Publication
    VAR_025460
    Natural varianti102 – 1021R → S in RP43. 1 Publication
    VAR_025461
    Natural varianti344 – 3441S → R in RP43. 1 Publication
    VAR_006049
    Natural varianti569 – 5691Q → K in RP43. 1 Publication
    VAR_025466
    Natural varianti573 – 5731S → P in RP43. 1 Publication
    VAR_025467

    Keywords - Diseasei

    Disease mutation, Retinitis pigmentosa

    Organism-specific databases

    MIMi613810. phenotype.
    Orphaneti791. Retinitis pigmentosa.
    PharmGKBiPA33133.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 857856Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alphaPRO_0000198828Add
    BLAST
    Propeptidei858 – 8603Removed in mature formBy similarityPRO_0000396697

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylglycineBy similarity
    Modified residuei857 – 8571Cysteine methyl esterBy similarity
    Lipidationi857 – 8571S-farnesyl cysteineBy similarity

    Keywords - PTMi

    Acetylation, Lipoprotein, Methylation, Prenylation

    Proteomic databases

    PaxDbiP16499.
    PRIDEiP16499.

    PTM databases

    PhosphoSiteiP16499.

    Miscellaneous databases

    PMAP-CutDBP16499.

    Expressioni

    Gene expression databases

    ArrayExpressiP16499.
    BgeeiP16499.
    CleanExiHS_PDE6A.
    GenevestigatoriP16499.

    Organism-specific databases

    HPAiHPA016970.

    Interactioni

    Subunit structurei

    Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain.

    Protein-protein interaction databases

    BioGridi111171. 1 interaction.
    STRINGi9606.ENSP00000255266.

    Structurei

    3D structure databases

    ProteinModelPortaliP16499.
    SMRiP16499. Positions 31-816.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini73 – 222150GAF 1Add
    BLAST
    Domaini254 – 431178GAF 2Add
    BLAST

    Sequence similaritiesi

    Contains 2 GAF domains.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiNOG242608.
    HOGENOMiHOG000007069.
    HOVERGENiHBG053539.
    InParanoidiP16499.
    KOiK08718.
    OMAiQMYYELK.
    OrthoDBiEOG7BGHK1.
    PhylomeDBiP16499.
    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.

    P16499-1 [UniParc]FASTAAdd to Basket

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    MGEVTAEEVE KFLDSNIGFA KQYYNLHYRA KLISDLLGAK EAAVDFSNYH    50
    SPSSMEESEI IFDLLRDFQE NLQTEKCIFN VMKKLCFLLQ ADRMSLFMYR 100
    TRNGIAELAT RLFNVHKDAV LEDCLVMPDQ EIVFPLDMGI VGHVAHSKKI 150
    ANVPNTEEDE HFCDFVDILT EYKTKNILAS PIMNGKDVVA IIMAVNKVDG 200
    SHFTKRDEEI LLKYLNFANL IMKVYHLSYL HNCETRRGQI LLWSGSKVFE 250
    ELTDIERQFH KALYTVRAFL NCDRYSVGLL DMTKQKEFFD VWPVLMGEVP 300
    PYSGPRTPDG REINFYKVID YILHGKEDIK VIPNPPPDHW ALVSGLPAYV 350
    AQNGLICNIM NAPAEDFFAF QKEPLDESGW MIKNVLSMPI VNKKEEIVGV 400
    ATFYNRKDGK PFDEMDETLM ESLTQFLGWS VLNPDTYESM NKLENRKDIF 450
    QDIVKYHVKC DNEEIQKILK TREVYGKEPW ECEEEELAEI LQAELPDADK 500
    YEINKFHFSD LPLTELELVK CGIQMYYELK VVDKFHIPQE ALVRFMYSLS 550
    KGYRKITYHN WRHGFNVGQT MFSLLVTGKL KRYFTDLEAL AMVTAAFCHD 600
    IDHRGTNNLY QMKSQNPLAK LHGSSILERH HLEFGKTLLR DESLNIFQNL 650
    NRRQHEHAIH MMDIAIIATD LALYFKKRTM FQKIVDQSKT YESEQEWTQY 700
    MMLEQTRKEI VMAMMMTACD LSAITKPWEV QSQVALLVAA EFWEQGDLER 750
    TVLQQNPIPM MDRNKADELP KLQVGFIDFV CTFVYKEFSR FHEEITPMLD 800
    GITNNRKEWK ALADEYDAKM KVQEEKKQKQ QSAKSAAAGN QPGGNPSPGG 850
    ATTSKSCCIQ 860
    Length:860
    Mass (Da):99,547
    Last modified:November 25, 2008 - v4
    Checksum:i7EEA48A234C1FE59
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti224 – 2241V → W in AAB69155. (PubMed:2155175)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti102 – 1021R → H in RP43. 1 Publication
    VAR_025460
    Natural varianti102 – 1021R → S in RP43. 1 Publication
    VAR_025461
    Natural varianti145 – 1451A → T.
    Corresponds to variant rs35431421 [ dbSNP | Ensembl ].
    VAR_047730
    Natural varianti216 – 2161N → S.1 Publication
    Corresponds to variant rs10057110 [ dbSNP | Ensembl ].
    VAR_025462
    Natural varianti277 – 2771V → A.1 Publication
    VAR_025463
    Natural varianti293 – 2931P → L.1 Publication
    Corresponds to variant rs114973968 [ dbSNP | Ensembl ].
    VAR_025464
    Natural varianti344 – 3441S → R in RP43. 1 Publication
    VAR_006049
    Natural varianti391 – 3911V → M.1 Publication
    Corresponds to variant rs61732059 [ dbSNP | Ensembl ].
    VAR_025465
    Natural varianti492 – 4921Q → H.
    Corresponds to variant rs17711594 [ dbSNP | Ensembl ].
    VAR_047731
    Natural varianti569 – 5691Q → K in RP43. 1 Publication
    VAR_025466
    Natural varianti573 – 5731S → P in RP43. 1 Publication
    VAR_025467
    Natural varianti827 – 8271K → Q.1 Publication
    VAR_025468
    Natural varianti850 – 8501G → V.1 Publication
    Corresponds to variant rs138315990 [ dbSNP | Ensembl ].
    VAR_025469

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M26061 mRNA. Translation: AAB69155.1.
    CH471062 Genomic DNA. Translation: EAW61757.1.
    BC035909 mRNA. Translation: AAH35909.1.
    CCDSiCCDS4299.1.
    PIRiB34611.
    RefSeqiNP_000431.2. NM_000440.2.
    UniGeneiHs.567314.

    Genome annotation databases

    EnsembliENST00000255266; ENSP00000255266; ENSG00000132915.
    GeneIDi5145.
    KEGGihsa:5145.
    UCSCiuc003lrg.4. human.

    Polymorphism databases

    DMDMi215274230.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Web resourcesi

    Mutations of the PDE6A/B/G genes

    Retina International's Scientific Newsletter

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M26061 mRNA. Translation: AAB69155.1 .
    CH471062 Genomic DNA. Translation: EAW61757.1 .
    BC035909 mRNA. Translation: AAH35909.1 .
    CCDSi CCDS4299.1.
    PIRi B34611.
    RefSeqi NP_000431.2. NM_000440.2.
    UniGenei Hs.567314.

    3D structure databases

    ProteinModelPortali P16499.
    SMRi P16499. Positions 31-816.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 111171. 1 interaction.
    STRINGi 9606.ENSP00000255266.

    Chemistry

    BindingDBi P16499.
    ChEMBLi CHEMBL2097163.

    PTM databases

    PhosphoSitei P16499.

    Polymorphism databases

    DMDMi 215274230.

    Proteomic databases

    PaxDbi P16499.
    PRIDEi P16499.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000255266 ; ENSP00000255266 ; ENSG00000132915 .
    GeneIDi 5145.
    KEGGi hsa:5145.
    UCSCi uc003lrg.4. human.

    Organism-specific databases

    CTDi 5145.
    GeneCardsi GC05M149220.
    GeneReviewsi PDE6A.
    HGNCi HGNC:8785. PDE6A.
    HPAi HPA016970.
    MIMi 180071. gene.
    613810. phenotype.
    neXtProti NX_P16499.
    Orphaneti 791. Retinitis pigmentosa.
    PharmGKBi PA33133.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG242608.
    HOGENOMi HOG000007069.
    HOVERGENi HBG053539.
    InParanoidi P16499.
    KOi K08718.
    OMAi QMYYELK.
    OrthoDBi EOG7BGHK1.
    PhylomeDBi P16499.
    TreeFami TF316499.

    Enzyme and pathway databases

    Reactomei REACT_163919. Inactivation, recovery and regulation of the phototransduction cascade.
    REACT_163932. Activation of the phototransduction cascade.
    REACT_172761. Ca2+ pathway.

    Miscellaneous databases

    GeneWikii PDE6A.
    GenomeRNAii 5145.
    NextBioi 19852.
    PMAP-CutDB P16499.
    PROi P16499.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P16499.
    Bgeei P16499.
    CleanExi HS_PDE6A.
    Genevestigatori P16499.

    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. "Molecular characterization of human and bovine rod photoreceptor cGMP phosphodiesterase alpha-subunit and chromosomal localization of the human gene."
      Pittler S.J., Baehr W., Wasmuth J.J., McConnell D.G., Champagne M.S., VanTuinen P., Ledbetter D., Davis R.L.
      Genomics 6:272-283(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. Pittler S.J., Baehr W., Wasmuth J.J., McConnell D.G., Champagne M.S., Vantuinen P., Ledbetter D., Davis R.L.
      Submitted (MAY-1995) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION TO 846-849.
    3. 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: Eye.
    5. "Autosomal recessive retinitis pigmentosa caused by mutations in the alpha subunit of rod cGMP phosphodiesterase."
      Huang S.H., Pittler S.J., Huang X., Oliveira L., Berson E.L., Dryja T.P.
      Nat. Genet. 11:468-471(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT RP43 ARG-344.
    6. "Frequency of mutations in the gene encoding the alpha subunit of rod cGMP-phosphodiesterase in autosomal recessive retinitis pigmentosa."
      Dryja T.P., Rucinski D.E., Chen S.H., Berson E.L.
      Invest. Ophthalmol. Vis. Sci. 40:1859-1865(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANTS RP43 HIS-102; SER-102; LYS-569 AND PRO-573, VARIANTS SER-216; ALA-277; LEU-293; MET-391; GLN-827 AND VAL-850.

    Entry informationi

    Entry nameiPDE6A_HUMAN
    AccessioniPrimary (citable) accession number: P16499
    Secondary accession number(s): Q0P638
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: November 25, 2008
    Last modified: October 1, 2014
    This is version 145 of the entry and version 4 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

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 5
      Human chromosome 5: 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3