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O43924

- PDE6D_HUMAN

UniProt

O43924 - PDE6D_HUMAN

Protein

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Gene

PDE6D

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 127 (01 Oct 2014)
      Sequence version 1 (01 Jun 1998)
      Previous versions | rss
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    Functioni

    Acts as a GTP specific dissociation inhibitor (GDI). Increases the affinity of ARL3 for GTP by several orders of magnitude and does so by decreasing the nucleotide dissociation rate. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation By similarity.By similarity

    GO - Molecular functioni

    1. 3',5'-cyclic-nucleotide phosphodiesterase activity Source: InterPro
    2. GTPase inhibitor activity Source: UniProtKB
    3. protein binding Source: UniProtKB
    4. Rab GTPase binding Source: UniProtKB

    GO - Biological processi

    1. negative regulation of catalytic activity Source: GOC
    2. regulation of GTP catabolic process Source: UniProtKB
    3. response to stimulus Source: UniProtKB-KW
    4. visual perception Source: ProtInc

    Keywords - Biological processi

    Sensory transduction, Vision

    Keywords - Ligandi

    cGMP

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
    Short name:
    GMP-PDE delta
    Alternative name(s):
    Protein p17
    Gene namesi
    Name:PDE6D
    Synonyms:PDED
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:8788. PDE6D.

    Subcellular locationi

    Cytoplasmcytosol 1 Publication. Cytoplasmic vesicle membrane 1 Publication; Peripheral membrane protein 1 Publication

    GO - Cellular componenti

    1. cytoplasmic vesicle Source: UniProtKB
    2. cytoplasmic vesicle membrane Source: UniProtKB-SubCell
    3. cytosol Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Cytoplasmic vesicle, Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Joubert syndrome 22 (JBTS22) [MIM:615665]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.

    Keywords - Diseasei

    Ciliopathy, Joubert syndrome

    Organism-specific databases

    MIMi615665. phenotype.
    Orphaneti2754. Joubert syndrome with orofaciodigital defect.
    PharmGKBiPA33136.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 150150Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit deltaPRO_0000221208Add
    BLAST

    Proteomic databases

    MaxQBiO43924.
    PaxDbiO43924.
    PRIDEiO43924.

    Expressioni

    Tissue specificityi

    Widely expressed. Detected in various tissues including spleen, prostate gland, testis, ovary, small intestine, colon, retina, and peripheral blood.1 Publication

    Gene expression databases

    ArrayExpressiO43924.
    BgeeiO43924.
    CleanExiHS_PDE6D.
    GenevestigatoriO43924.

    Organism-specific databases

    HPAiHPA037434.

    Interactioni

    Subunit structurei

    Interacts with ARL2, ARL3, and RPGR. Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain. Interacts with ARL3; the interaction occurs specifically with the GTP-bound form of ARL3 By similarity. Interacts with HRAS and RPGR. Interacts with RAB13 (isoprenylated form); dissociates RAB13 from membranes.By similarity4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ARL2P364044EBI-712685,EBI-752365
    Arl2Q9D0J46EBI-712685,EBI-1033319From a different organism.
    ARL3P364052EBI-712685,EBI-712710
    Arl3Q9WUL74EBI-712685,EBI-6860857From a different organism.
    RAB13P511532EBI-712685,EBI-1780121
    RHEBQ153825EBI-712685,EBI-6860739
    RPGRQ928349EBI-712685,EBI-6558417

    Protein-protein interaction databases

    BioGridi111173. 23 interactions.
    DIPiDIP-36660N.
    IntActiO43924. 13 interactions.
    MINTiMINT-236371.
    STRINGi9606.ENSP00000287600.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1311
    Beta strandi15 – 2410
    Turni25 – 273
    Beta strandi30 – 345
    Beta strandi43 – 508
    Helixi51 – 555
    Beta strandi57 – 6913
    Beta strandi71 – 8212
    Beta strandi85 – 9713
    Beta strandi101 – 11010
    Helixi114 – 1163
    Helixi120 – 1234
    Turni124 – 1263
    Beta strandi127 – 1359
    Beta strandi138 – 15013

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KSGX-ray2.30B1-150[»]
    1KSHX-ray1.80B1-150[»]
    1KSJX-ray2.60B1-150[»]
    3T5GX-ray1.70B1-150[»]
    3T5IX-ray2.10A/B/C/D1-150[»]
    4JHPX-ray1.90B1-150[»]
    4JV6X-ray1.87B1-150[»]
    4JV8X-ray1.45B1-150[»]
    4JVBX-ray1.75B1-150[»]
    4JVFX-ray2.40B1-150[»]
    ProteinModelPortaliO43924.
    SMRiO43924. Positions 4-150.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO43924.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni144 – 1507Required for association with membranes

    Sequence similaritiesi

    Belongs to the PDE6D/unc-119 family.Curated

    Phylogenomic databases

    eggNOGiNOG302334.
    HOGENOMiHOG000007689.
    HOVERGENiHBG053542.
    InParanoidiO43924.
    KOiK13758.
    OMAiEEWFFDF.
    OrthoDBiEOG7HMS2N.
    PhylomeDBiO43924.
    TreeFamiTF314474.

    Family and domain databases

    Gene3Di2.70.50.40. 1 hit.
    InterProiIPR008015. GMP_PDE_delta.
    IPR014756. Ig_E-set.
    IPR017287. Rhodop-sen_GMP-Pdiesterase_dsu.
    [Graphical view]
    PfamiPF05351. GMP_PDE_delta. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037825. GMP-Pdiesterase_delta. 1 hit.
    SUPFAMiSSF81296. SSF81296. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O43924-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSAKDERARE ILRGFKLNWM NLRDAETGKI LWQGTEDLSV PGVEHEARVP    50
    KKILKCKAVS RELNFSSTEQ MEKFRLEQKV YFKGQCLEEW FFEFGFVIPN 100
    STNTWQSLIE AAPESQMMPA SVLTGNVIIE TKFFDDDLLV STSRVRLFYV 150
    Length:150
    Mass (Da):17,420
    Last modified:June 1, 1998 - v1
    Checksum:iAB8D9309C33B4411
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti117 – 1171M → V in CAA04880. (PubMed:9712853)Curated
    Sequence conflicti146 – 1461R → G in CAA04880. (PubMed:9712853)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF045999 Genomic DNA. Translation: AAC39720.1.
    AF022912 mRNA. Translation: AAB87872.1.
    AF042835, AF042833, AF042834 Genomic DNA. Translation: AAC25953.1.
    AJ001626 mRNA. Translation: CAA04880.1.
    BT007278 mRNA. Translation: AAP35942.1.
    BC007831 mRNA. Translation: AAH07831.1.
    CCDSiCCDS33398.1.
    RefSeqiNP_001277947.1. NM_001291018.1.
    NP_002592.1. NM_002601.3.
    UniGeneiHs.516808.

    Genome annotation databases

    EnsembliENST00000287600; ENSP00000287600; ENSG00000156973.
    GeneIDi5147.
    KEGGihsa:5147.
    UCSCiuc002vse.1. human.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF045999 Genomic DNA. Translation: AAC39720.1 .
    AF022912 mRNA. Translation: AAB87872.1 .
    AF042835 , AF042833 , AF042834 Genomic DNA. Translation: AAC25953.1 .
    AJ001626 mRNA. Translation: CAA04880.1 .
    BT007278 mRNA. Translation: AAP35942.1 .
    BC007831 mRNA. Translation: AAH07831.1 .
    CCDSi CCDS33398.1.
    RefSeqi NP_001277947.1. NM_001291018.1.
    NP_002592.1. NM_002601.3.
    UniGenei Hs.516808.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1KSG X-ray 2.30 B 1-150 [» ]
    1KSH X-ray 1.80 B 1-150 [» ]
    1KSJ X-ray 2.60 B 1-150 [» ]
    3T5G X-ray 1.70 B 1-150 [» ]
    3T5I X-ray 2.10 A/B/C/D 1-150 [» ]
    4JHP X-ray 1.90 B 1-150 [» ]
    4JV6 X-ray 1.87 B 1-150 [» ]
    4JV8 X-ray 1.45 B 1-150 [» ]
    4JVB X-ray 1.75 B 1-150 [» ]
    4JVF X-ray 2.40 B 1-150 [» ]
    ProteinModelPortali O43924.
    SMRi O43924. Positions 4-150.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 111173. 23 interactions.
    DIPi DIP-36660N.
    IntActi O43924. 13 interactions.
    MINTi MINT-236371.
    STRINGi 9606.ENSP00000287600.

    Chemistry

    BindingDBi O43924.
    ChEMBLi CHEMBL2097163.

    Proteomic databases

    MaxQBi O43924.
    PaxDbi O43924.
    PRIDEi O43924.

    Protocols and materials databases

    DNASUi 5147.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000287600 ; ENSP00000287600 ; ENSG00000156973 .
    GeneIDi 5147.
    KEGGi hsa:5147.
    UCSCi uc002vse.1. human.

    Organism-specific databases

    CTDi 5147.
    GeneCardsi GC02M232597.
    HGNCi HGNC:8788. PDE6D.
    HPAi HPA037434.
    MIMi 602676. gene.
    615665. phenotype.
    neXtProti NX_O43924.
    Orphaneti 2754. Joubert syndrome with orofaciodigital defect.
    PharmGKBi PA33136.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG302334.
    HOGENOMi HOG000007689.
    HOVERGENi HBG053542.
    InParanoidi O43924.
    KOi K13758.
    OMAi EEWFFDF.
    OrthoDBi EOG7HMS2N.
    PhylomeDBi O43924.
    TreeFami TF314474.

    Miscellaneous databases

    ChiTaRSi PDE6D. human.
    EvolutionaryTracei O43924.
    GeneWikii PDE6D.
    GenomeRNAii 5147.
    NextBioi 19860.
    PROi O43924.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O43924.
    Bgeei O43924.
    CleanExi HS_PDE6D.
    Genevestigatori O43924.

    Family and domain databases

    Gene3Di 2.70.50.40. 1 hit.
    InterProi IPR008015. GMP_PDE_delta.
    IPR014756. Ig_E-set.
    IPR017287. Rhodop-sen_GMP-Pdiesterase_dsu.
    [Graphical view ]
    Pfami PF05351. GMP_PDE_delta. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037825. GMP-Pdiesterase_delta. 1 hit.
    SUPFAMi SSF81296. SSF81296. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Characterization of human and mouse rod cGMP phosphodiesterase delta subunit (PDE6D) and chromosomal localization of the human gene."
      Li N., Florio S.K., Pettenati M.J., Rao P.N., Beavo J.A., Baehr W.
      Genomics 49:76-82(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "cDNA sequence, genomic organization and mapping of PDE6D, the human gene encoding the delta subunit of the cGMP phosphodiesterase of retinal rod cells to chromosome 2q36."
      Erchova G., Derre J., Chatelin S., Nancy V., Berger R., Kaplan J., Munnich A., de Gunzburg J.
      Cytogenet. Cell Genet. 79:139-141(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. "Cloning and gene structure of the rod cGMP phosphodiesterase delta subunit gene (PDED) in man and mouse."
      Lorenz B., Migliaccio C., Lichtner P., Meyer C., Strom T.M., D'Urso M., Becker J., Ciccodicola A., Meitinger T.
      Eur. J. Hum. Genet. 6:283-290(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. "The rod cGMP phosphodiesterase delta subunit dissociates the small GTPase Rab13 from membranes."
      Marzesco A.M., Galli T., Louvard D., Zahraoui A.
      J. Biol. Chem. 273:22340-22345(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], INTERACTION WITH RAB13, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
    5. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
      Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
      Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "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.
    7. "The delta subunit of rod specific cyclic GMP phosphodiesterase, PDE delta, interacts with the Arf-like protein Arl3 in a GTP specific manner."
      Linari M., Hanzal-Bayer M., Becker J.
      FEBS Lett. 458:55-59(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH ARL3.
    8. "The retinitis pigmentosa GTPase regulator, RPGR, interacts with the delta subunit of rod cyclic GMP phosphodiesterase."
      Linari M., Ueffing M., Manson F., Wright A., Meitinger T., Becker J.
      Proc. Natl. Acad. Sci. U.S.A. 96:1315-1320(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RPGR.
    9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. Cited for: INVOLVEMENT IN JBTS22.
    11. "The complex of Arl2-GTP and PDE delta: from structure to function."
      Hanzal-Bayer M., Renault L., Roversi P., Wittinghofer A., Hillig R.C.
      EMBO J. 21:2095-2106(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH MOUSE ARL2 AND GTP, INTERACTION WITH HRAS.

    Entry informationi

    Entry nameiPDE6D_HUMAN
    AccessioniPrimary (citable) accession number: O43924
    Secondary accession number(s): O43250
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: June 1, 1998
    Last modified: October 1, 2014
    This is version 127 of the entry and version 1 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 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3