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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)DescriptionActionsGraphical viewLength
Active sitei559Proton donorBy similarity1
Metal bindingi563Divalent metal cation 1By similarity1
Metal bindingi599Divalent metal cation 1By similarity1
Metal bindingi600Divalent metal cation 1By similarity1
Metal bindingi600Divalent metal cation 2By similarity1
Metal bindingi720Divalent metal cation 1By similarity1

GO - Molecular functioni

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

GO - Biological processi

  • GMP metabolic process Source: BHF-UCL
  • regulation of cytosolic calcium ion concentration Source: BHF-UCL
  • regulation of rhodopsin mediated signaling pathway Source: Reactome
  • rhodopsin mediated signaling pathway Source: Reactome
  • visual perception Source: ProtInc
  • Wnt signaling pathway, calcium modulating pathway Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Sensory transduction, Vision

Keywords - Ligandi

cGMP, Metal-binding

Enzyme and pathway databases

BioCyciZFISH:HS05708-MONOMER.
ReactomeiR-HSA-2485179. Activation of the phototransduction cascade.
R-HSA-2514859. Inactivation, recovery and regulation of the phototransduction cascade.
R-HSA-4086398. 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
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8785. PDE6A.

Subcellular locationi

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Natural variantiVAR_025460102R → H in RP43. 1 PublicationCorresponds to variant rs750539462dbSNPEnsembl.1
Natural variantiVAR_025461102R → S in RP43. 1 PublicationCorresponds to variant rs141252097dbSNPEnsembl.1
Natural variantiVAR_006049344S → R in RP43. 1 PublicationCorresponds to variant rs121918577dbSNPEnsembl.1
Natural variantiVAR_025466569Q → K in RP43. 1 PublicationCorresponds to variant rs139444207dbSNPEnsembl.1
Natural variantiVAR_025467573S → P in RP43. 1 PublicationCorresponds to variant rs755527251dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi5145.
MalaCardsiPDE6A.
MIMi613810. phenotype.
OpenTargetsiENSG00000132915.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA33133.

Chemistry databases

ChEMBLiCHEMBL3878.
DrugBankiDB00201. Caffeine.
GuidetoPHARMACOLOGYi1312.

Polymorphism and mutation databases

BioMutaiPDE6A.
DMDMi215274230.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00001988282 – 857Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alphaAdd BLAST856
PropeptideiPRO_0000396697858 – 860Removed in mature formBy similarity3

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylglycineBy similarity1
Modified residuei857Cysteine methyl esterBy similarity1
Lipidationi857S-farnesyl cysteineBy similarity1

Keywords - PTMi

Acetylation, Lipoprotein, Methylation, Prenylation

Proteomic databases

EPDiP16499.
PaxDbiP16499.
PeptideAtlasiP16499.
PRIDEiP16499.

PTM databases

iPTMnetiP16499.
PhosphoSitePlusiP16499.

Miscellaneous databases

PMAP-CutDBP16499.

Expressioni

Gene expression databases

BgeeiENSG00000132915.
CleanExiHS_PDE6A.
ExpressionAtlasiP16499. baseline and differential.
GenevisibleiP16499. HS.

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. 4 interactors.
STRINGi9606.ENSP00000255266.

Chemistry databases

BindingDBiP16499.

Structurei

3D structure databases

ProteinModelPortaliP16499.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini73 – 222GAF 1Add BLAST150
Domaini254 – 431GAF 2Add BLAST178

Sequence similaritiesi

Contains 2 GAF domains.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3689. Eukaryota.
ENOG410XRI7. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
KOiK08718.
OMAiFAKQYYN.
OrthoDBiEOG091G01RK.
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.
IPR032958. PDE6A.
IPR023088. PDEase.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view]
PANTHERiPTHR11347:SF115. PTHR11347:SF115. 2 hits.
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)DescriptionActionsGraphical viewLength
Sequence conflicti224V → W in AAB69155 (PubMed:2155175).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_025460102R → H in RP43. 1 PublicationCorresponds to variant rs750539462dbSNPEnsembl.1
Natural variantiVAR_025461102R → S in RP43. 1 PublicationCorresponds to variant rs141252097dbSNPEnsembl.1
Natural variantiVAR_047730145A → T.Corresponds to variant rs35431421dbSNPEnsembl.1
Natural variantiVAR_025462216N → S.1 PublicationCorresponds to variant rs10057110dbSNPEnsembl.1
Natural variantiVAR_025463277V → A.1 PublicationCorresponds to variant rs145608358dbSNPEnsembl.1
Natural variantiVAR_025464293P → L.1 PublicationCorresponds to variant rs114973968dbSNPEnsembl.1
Natural variantiVAR_006049344S → R in RP43. 1 PublicationCorresponds to variant rs121918577dbSNPEnsembl.1
Natural variantiVAR_025465391V → M.1 PublicationCorresponds to variant rs61732059dbSNPEnsembl.1
Natural variantiVAR_047731492Q → H.Corresponds to variant rs17711594dbSNPEnsembl.1
Natural variantiVAR_025466569Q → K in RP43. 1 PublicationCorresponds to variant rs139444207dbSNPEnsembl.1
Natural variantiVAR_025467573S → P in RP43. 1 PublicationCorresponds to variant rs755527251dbSNPEnsembl.1
Natural variantiVAR_025468827K → Q.1 PublicationCorresponds to variant rs780450680dbSNPEnsembl.1
Natural variantiVAR_025469850G → V.1 PublicationCorresponds to variant rs138315990dbSNPEnsembl.1

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.

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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111171. 4 interactors.
STRINGi9606.ENSP00000255266.

Chemistry databases

BindingDBiP16499.
ChEMBLiCHEMBL3878.
DrugBankiDB00201. Caffeine.
GuidetoPHARMACOLOGYi1312.

PTM databases

iPTMnetiP16499.
PhosphoSitePlusiP16499.

Polymorphism and mutation databases

BioMutaiPDE6A.
DMDMi215274230.

Proteomic databases

EPDiP16499.
PaxDbiP16499.
PeptideAtlasiP16499.
PRIDEiP16499.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi5145.
DisGeNETi5145.
GeneCardsiPDE6A.
GeneReviewsiPDE6A.
HGNCiHGNC:8785. PDE6A.
HPAiHPA016970.
MalaCardsiPDE6A.
MIMi180071. gene.
613810. phenotype.
neXtProtiNX_P16499.
OpenTargetsiENSG00000132915.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA33133.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3689. Eukaryota.
ENOG410XRI7. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
KOiK08718.
OMAiFAKQYYN.
OrthoDBiEOG091G01RK.
PhylomeDBiP16499.
TreeFamiTF316499.

Enzyme and pathway databases

BioCyciZFISH:HS05708-MONOMER.
ReactomeiR-HSA-2485179. Activation of the phototransduction cascade.
R-HSA-2514859. Inactivation, recovery and regulation of the phototransduction cascade.
R-HSA-4086398. Ca2+ pathway.

Miscellaneous databases

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

Gene expression databases

BgeeiENSG00000132915.
CleanExiHS_PDE6A.
ExpressionAtlasiP16499. baseline and differential.
GenevisibleiP16499. HS.

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.
IPR032958. PDE6A.
IPR023088. PDEase.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view]
PANTHERiPTHR11347:SF115. PTHR11347:SF115. 2 hits.
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...

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: November 2, 2016
This is version 165 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

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 one 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.