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Protein

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

Gene

PDE6A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

a divalent metal cationBy similarityNote: 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

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
Complete GO annotation...

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_263982. 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 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8785. PDE6A.

Subcellular locationi

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

GO - Cellular componenti

  1. photoreceptor disc membrane Source: Reactome
  2. plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Involvement in diseasei

Retinitis pigmentosa 43 (RP43)2 Publications

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA 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.

See also OMIM:613810
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.

Chemistry

DrugBankiDB00201. Caffeine.

Polymorphism and mutation databases

BioMutaiPDE6A.
DMDMi215274230.

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

BgeeiP16499.
CleanExiHS_PDE6A.
ExpressionAtlasiP16499. baseline and differential.
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 31-815.
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.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
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

« Hide

        10         20         30         40         50
MGEVTAEEVE KFLDSNIGFA KQYYNLHYRA KLISDLLGAK EAAVDFSNYH
60 70 80 90 100
SPSSMEESEI IFDLLRDFQE NLQTEKCIFN VMKKLCFLLQ ADRMSLFMYR
110 120 130 140 150
TRNGIAELAT RLFNVHKDAV LEDCLVMPDQ EIVFPLDMGI VGHVAHSKKI
160 170 180 190 200
ANVPNTEEDE HFCDFVDILT EYKTKNILAS PIMNGKDVVA IIMAVNKVDG
210 220 230 240 250
SHFTKRDEEI LLKYLNFANL IMKVYHLSYL HNCETRRGQI LLWSGSKVFE
260 270 280 290 300
ELTDIERQFH KALYTVRAFL NCDRYSVGLL DMTKQKEFFD VWPVLMGEVP
310 320 330 340 350
PYSGPRTPDG REINFYKVID YILHGKEDIK VIPNPPPDHW ALVSGLPAYV
360 370 380 390 400
AQNGLICNIM NAPAEDFFAF QKEPLDESGW MIKNVLSMPI VNKKEEIVGV
410 420 430 440 450
ATFYNRKDGK PFDEMDETLM ESLTQFLGWS VLNPDTYESM NKLENRKDIF
460 470 480 490 500
QDIVKYHVKC DNEEIQKILK TREVYGKEPW ECEEEELAEI LQAELPDADK
510 520 530 540 550
YEINKFHFSD LPLTELELVK CGIQMYYELK VVDKFHIPQE ALVRFMYSLS
560 570 580 590 600
KGYRKITYHN WRHGFNVGQT MFSLLVTGKL KRYFTDLEAL AMVTAAFCHD
610 620 630 640 650
IDHRGTNNLY QMKSQNPLAK LHGSSILERH HLEFGKTLLR DESLNIFQNL
660 670 680 690 700
NRRQHEHAIH MMDIAIIATD LALYFKKRTM FQKIVDQSKT YESEQEWTQY
710 720 730 740 750
MMLEQTRKEI VMAMMMTACD LSAITKPWEV QSQVALLVAA EFWEQGDLER
760 770 780 790 800
TVLQQNPIPM MDRNKADELP KLQVGFIDFV CTFVYKEFSR FHEEITPMLD
810 820 830 840 850
GITNNRKEWK ALADEYDAKM KVQEEKKQKQ QSAKSAAAGN QPGGNPSPGG
860
ATTSKSCCIQ
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:
EMBLi
GenBanki
DDBJi
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 and mutation databases

BioMutaiPDE6A.

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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP16499.
SMRiP16499. Positions 31-815.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111171. 1 interaction.
STRINGi9606.ENSP00000255266.

Chemistry

BindingDBiP16499.
ChEMBLiCHEMBL2095220.
DrugBankiDB00201. Caffeine.

PTM databases

PhosphoSiteiP16499.

Polymorphism and mutation databases

BioMutaiPDE6A.
DMDMi215274230.

Proteomic databases

PaxDbiP16499.
PRIDEiP16499.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi5145.
GeneCardsiGC05M149220.
GeneReviewsiPDE6A.
HGNCiHGNC:8785. PDE6A.
HPAiHPA016970.
MIMi180071. gene.
613810. phenotype.
neXtProtiNX_P16499.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA33133.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG242608.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
KOiK08718.
OMAiQMYYELK.
OrthoDBiEOG7BGHK1.
PhylomeDBiP16499.
TreeFamiTF316499.

Enzyme and pathway databases

ReactomeiREACT_163919. Inactivation, recovery and regulation of the phototransduction cascade.
REACT_163932. Activation of the phototransduction cascade.
REACT_263982. Ca2+ pathway.

Miscellaneous databases

ChiTaRSiPDE6A. human.
GeneWikiiPDE6A.
GenomeRNAii5145.
NextBioi19852.
PMAP-CutDBP16499.
PROiP16499.
SOURCEiSearch...

Gene expression databases

BgeeiP16499.
CleanExiHS_PDE6A.
ExpressionAtlasiP16499. baseline and differential.
GenevestigatoriP16499.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: April 29, 2015
This is version 151 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.