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O43924 (PDE6D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Short name=GMP-PDE delta
Alternative name(s):
Protein p17
Gene names
Name:PDE6D
Synonyms:PDED
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length150 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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. Ref.4 Ref.7 Ref.8 Ref.10

Subcellular location

Cytoplasmcytosol. Cytoplasmic vesicle membrane; Peripheral membrane protein Ref.4.

Tissue specificity

Widely expressed. Detected in various tissues including spleen, prostate gland, testis, ovary, small intestine, colon, retina, and peripheral blood. Ref.4

Sequence similarities

Belongs to the PDE6D/unc-119 family.

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 150150Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
PRO_0000221208

Regions

Region144 – 1507Required for association with membranes

Experimental info

Sequence conflict1171M → V in CAA04880. Ref.4
Sequence conflict1461R → G in CAA04880. Ref.4

Secondary structure

.......................... 150
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O43924 [UniParc].

Last modified June 1, 1998. Version 1.
Checksum: AB8D9309C33B4411

FASTA15017,420
        10         20         30         40         50         60 
MSAKDERARE ILRGFKLNWM NLRDAETGKI LWQGTEDLSV PGVEHEARVP KKILKCKAVS 

        70         80         90        100        110        120 
RELNFSSTEQ MEKFRLEQKV YFKGQCLEEW FFEFGFVIPN STNTWQSLIE AAPESQMMPA 

       130        140        150 
SVLTGNVIIE TKFFDDDLLV STSRVRLFYV 

« Hide

References

« Hide 'large scale' references
[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]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_002592.1. NM_002601.2.
UniGeneHs.516808.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalO43924.
SMRO43924. Positions 4-150.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111173. 23 interactions.
DIPDIP-36660N.
IntActO43924. 13 interactions.
MINTMINT-236371.
STRING9606.ENSP00000287600.

Chemistry

BindingDBO43924.
ChEMBLCHEMBL2363066.

Proteomic databases

PaxDbO43924.
PRIDEO43924.

Protocols and materials databases

DNASU5147.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000287600; ENSP00000287600; ENSG00000156973.
GeneID5147.
KEGGhsa:5147.
UCSCuc002vse.1. human.

Organism-specific databases

CTD5147.
GeneCardsGC02M232597.
HGNCHGNC:8788. PDE6D.
HPAHPA037434.
MIM602676. gene.
neXtProtNX_O43924.
PharmGKBPA33136.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG302334.
HOGENOMHOG000007689.
HOVERGENHBG053542.
InParanoidO43924.
KOK13758.
OMAGRIMEEW.
OrthoDBEOG7HMS2N.
PhylomeDBO43924.
TreeFamTF314474.

Gene expression databases

ArrayExpressO43924.
BgeeO43924.
CleanExHS_PDE6D.
GenevestigatorO43924.

Family and domain databases

Gene3D2.70.50.40. 1 hit.
InterProIPR008015. GMP_PDE_delta.
IPR014756. Ig_E-set.
IPR017287. Rhodop-sen_GMP-Pdiesterase_dsu.
[Graphical view]
PfamPF05351. GMP_PDE_delta. 1 hit.
[Graphical view]
PIRSFPIRSF037825. GMP-Pdiesterase_delta. 1 hit.
SUPFAMSSF81296. SSF81296. 1 hit.
ProtoNetSearch...

Other

ChiTaRSPDE6D. human.
EvolutionaryTraceO43924.
GeneWikiPDE6D.
GenomeRNAi5147.
NextBio19860.
PROO43924.
SOURCESearch...

Entry information

Entry namePDE6D_HUMAN
AccessionPrimary (citable) accession number: O43924
Secondary accession number(s): O43250
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: June 1, 1998
Last modified: April 16, 2014
This is version 123 of the entry and version 1 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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

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

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM