Reviewed,
UniProtKB/Swiss-Prot P16499 (PDE6A_HUMAN)
Last modified
February 9, 2010.
Version 101.
History...
Clusters with 100%,
90%,
50% identity |
Documents (5) |
Third-party data |
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Names and origin
| Protein names | Recommended name: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha Short name=GMP-PDE alpha EC=3.1.4.35 Alternative name(s): PDE V-B1 | ||||
| Gene names |
| ||||
| Organism | Homo sapiens (Human) [Complete proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 860 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is further processed into a mature form. |
| Protein existence | Evidence at protein level. |
General annotation (Comments)
| Function | This protein participates in processes of transmission and amplification of the visual signal. |
| Catalytic activity | Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate. |
| Cofactor | 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. |
| Subunit structure | Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain. |
| Subcellular location | Cell membrane; Lipid-anchor; Cytoplasmic side Potential. |
| Involvement in disease | Defects in PDE6A are a cause of retinitis pigmentosa autosomal recessive (ARRP) [MIM:268000]. RP leads to degeneration of retinal photoreceptor cells. 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. Ref.5 Ref.6 |
| Sequence similarities | Belongs to the cyclic nucleotide phosphodiesterase family. Contains 2 GAF domains. |
Ontologies
| Keywords | |
|---|---|
| Biological process | Sensory transduction Vision |
| Cellular component | Cell membrane Membrane |
| Coding sequence diversity | Polymorphism |
| Disease | Disease mutation Retinitis pigmentosa |
| Domain | Repeat |
| Ligand | Metal-binding cGMP |
| Molecular function | Hydrolase |
| PTM | Acetylation Lipoprotein Prenylation |
| Technical term | Complete proteome |
| Gene Ontology (GO) | |
| Biological process | response to stimulus Inferred from electronic annotation. Source: UniProtKB-KW signal transductionInferred from electronic annotation. Source: InterPro visual perception Ref.5Traceable author statement. Source: ProtInc |
| Cellular component | anchored to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membraneInferred from electronic annotation. Source: UniProtKB-KW |
| Molecular function | 3',5'-cyclic-GMP phosphodiesterase activity Inferred from electronic annotation. Source: EC |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Initiator methionine | 1 | 1 | Removed By similarity | ||||||
| Chain | 2 – 860 | 859 | Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha | PRO_0000198828 | |||||
Regions | |||||||||
| Domain | 73 – 222 | 150 | GAF 1 | ||||||
| Domain | 254 – 431 | 178 | GAF 2 | ||||||
Sites | |||||||||
| Active site | 559 | 1 | Proton donor By similarity | ||||||
| Metal binding | 563 | 1 | Divalent metal cation 1 By similarity | ||||||
| Metal binding | 599 | 1 | Divalent metal cation 1 By similarity | ||||||
| Metal binding | 600 | 1 | Divalent metal cation 1 By similarity | ||||||
| Metal binding | 600 | 1 | Divalent metal cation 2 By similarity | ||||||
| Metal binding | 720 | 1 | Divalent metal cation 1 By similarity | ||||||
Amino acid modifications | |||||||||
| Modified residue | 2 | 1 | N-acetylglycine By similarity | ||||||
| Lipidation | 857 | 1 | S-farnesyl cysteine By similarity | ||||||
Natural variations | |||||||||
| Natural variant | 102 | 1 | R → H in ARRP. Ref.6 | VAR_025460 | |||||
| Natural variant | 102 | 1 | R → S in ARRP. Ref.6 | VAR_025461 | |||||
| Natural variant | 145 | 1 | A → T: dbSNP rs35431421. | VAR_047730 | |||||
| Natural variant | 216 | 1 | N → S: dbSNP rs10057110. Ref.6 | VAR_025462 | |||||
| Natural variant | 277 | 1 | V → A | VAR_025463 | |||||
| Natural variant | 293 | 1 | P → L | VAR_025464 | |||||
| Natural variant | 344 | 1 | S → R in ARRP. Ref.5 | VAR_006049 | |||||
| Natural variant | 391 | 1 | V → M | VAR_025465 | |||||
| Natural variant | 492 | 1 | Q → H: dbSNP rs17711594. | VAR_047731 | |||||
| Natural variant | 569 | 1 | Q → K in ARRP. Ref.6 | VAR_025466 | |||||
| Natural variant | 573 | 1 | S → P in ARRP. Ref.6 | VAR_025467 | |||||
| Natural variant | 827 | 1 | K → Q | VAR_025468 | |||||
| Natural variant | 850 | 1 | G → V | VAR_025469 | |||||
Experimental info | |||||||||
| Sequence conflict | 224 | 1 | V → W in AAB69155. Ref.1 | ||||||
Sequences
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References
| « Hide 'large scale' references | |
| [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: 2155175] [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] | 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. Venter J.C.Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases 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: 15489334] [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: 7493036] [Abstract] Cited for: VARIANT ARRP 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: 10393062] [Abstract] Cited for: VARIANTS ARRP HIS-102; SER-102; LYS-569 AND PRO-573, VARIANTS SER-216; ALA-277; LEU-293; MET-391; GLN-827 AND VAL-850. |
| + | Additional computationally mapped references. |
Web resources
| Mutations of the PDE6A/B/G genes Retina International's Scientific Newsletter |
| GeneReviews |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | M26061 mRNA. Translation: AAB69155.1. CH471062 Genomic DNA. Translation: EAW61757.1. BC035909 mRNA. Translation: AAH35909.1. |
| IPI | IPI00218730. |
| PIR | B34611. |
| RefSeq | NP_000431.2. |
| UniGene | Hs.567314 |
3D structure databases | |
| SMR | P16499. Positions 64-444, 483-815. |
| ModBase | Search... |
Protein-protein interaction databases | |
| STRING | P16499. |
Proteomic databases | |
| PRIDE | P16499. |
Genome annotation databases | |
| Ensembl | ENST00000255266; ENSP00000255266; ENSG00000132915; Homo sapiens. [Genome view] |
| GeneID | 5145. |
| KEGG | hsa:5145. |
Organism-specific databases | |
| CTD | 5145. |
| GeneCards | GC05M149220. |
| H-InvDB | HIX0024840. |
| HGNC | HGNC:8785. PDE6A. |
| HPA | HPA016970. |
| MIM | 180071. gene. 268000. phenotype. |
| Orphanet | 791. Retinitis pigmentosa. |
| PharmGKB | PA33133. |
| GenAtlas | Search... |
Phylogenomic databases | |
| HOGENOM | HBG445272. |
| HOVERGEN | P16499. |
| InParanoid | P16499. |
| OMA | LIMKVFH. |
| OrthoDB | EOG97Q0R3. |
| PhylomeDB | P16499. |
Enzyme and pathway databases | |
| BRENDA | 3.1.4.35. 247. |
| Pathway_Interaction_DB | rhodopsin_pathway. Visual signal transduction: Rods. |
Gene expression databases | |
| ArrayExpress | P16499. |
| Bgee | P16499. |
| CleanEx | HS_PDE6A. |
| Genevestigator | P16499. |
| GermOnline | ENSG00000132915. Homo sapiens. |
Family and domain databases | |
| InterPro | IPR003018. GAF. IPR003607. Metal-dep_PHydrolase_HD_dom. IPR002073. PDEase. [Graphical view] |
| Pfam | PF01590. GAF. 2 hits. PF00233. PDEase_I. 1 hit. [Graphical view] |
| PRINTS | PR00387. PDIESTERASE1. |
| SMART | SM00065. GAF. 2 hits. SM00471. HDc. 1 hit. [Graphical view] |
| PROSITE | PS00126. PDEASE_I. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other Resources | |
| NextBio | 19852. |
| PMAP-CutDB | P16499. |
| SOURCE | Search... |
Entry information
| Entry name | PDE6A_HUMAN | ||||||||
| Accession | Primary (citable) accession number: P16499 Secondary accession number(s): Q0P638 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
| Disclaimer | Any 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 5 Human chromosome 5: 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 |
| SIMILARITY comments Index of protein domains and families |

Clusters with


