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Protein

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

Gene

PDE6A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionHydrolase
Biological processSensory transduction, Vision
LigandcGMP, Metal-binding

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000132915.10
HGNCiHGNC:8785 PDE6A
MIMi180071 gene
neXtProtiNX_P16499

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 dbSNP:rs750539462Ensembl.1
Natural variantiVAR_025461102R → S in RP43. 1 PublicationCorresponds to variant dbSNP:rs141252097EnsemblClinVar.1
Natural variantiVAR_006049344S → R in RP43. 1 PublicationCorresponds to variant dbSNP:rs121918577EnsemblClinVar.1
Natural variantiVAR_025466569Q → K in RP43. 1 PublicationCorresponds to variant dbSNP:rs139444207EnsemblClinVar.1
Natural variantiVAR_025467573S → P in RP43. 1 PublicationCorresponds to variant dbSNP:rs755527251Ensembl.1

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi5145
GeneReviewsiPDE6A
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

PaxDbiP16499
PeptideAtlasiP16499
PRIDEiP16499
ProteomicsDBi53376

PTM databases

iPTMnetiP16499
PhosphoSitePlusiP16499

Miscellaneous databases

PMAP-CutDBiP16499

Expressioni

Gene expression databases

BgeeiENSG00000132915 Expressed in 56 organ(s), highest expression level in retina
CleanExiHS_PDE6A
ExpressionAtlasiP16499 baseline and differential
GenevisibleiP16499 HS

Organism-specific databases

HPAiHPA016970
HPA074677

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
Domaini483 – 816PDEasePROSITE-ProRule annotationAdd BLAST334

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3689 Eukaryota
ENOG410XRI7 LUCA
GeneTreeiENSGT00760000119066
HOGENOMiHOG000007069
HOVERGENiHBG053539
KOiK08718
OMAiLICNIMN
OrthoDBiEOG091G01RK
PhylomeDBiP16499
TreeFamiTF316499

Family and domain databases

CDDicd00077 HDc, 1 hit
Gene3Di1.10.1300.10, 1 hit
3.30.450.40, 2 hits
InterProiView protein in InterPro
IPR003018 GAF
IPR029016 GAF-like_dom_sf
IPR003607 HD/PDEase_dom
IPR032958 PDE6A
IPR023088 PDEase
IPR002073 PDEase_catalytic_dom
IPR036971 PDEase_catalytic_dom_sf
IPR023174 PDEase_CS
PANTHERiPTHR11347:SF115 PTHR11347:SF115, 1 hit
PfamiView protein in Pfam
PF01590 GAF, 2 hits
PF00233 PDEase_I, 1 hit
PRINTSiPR00387 PDIESTERASE1
SMARTiView protein in SMART
SM00065 GAF, 2 hits
SM00471 HDc, 1 hit
PROSITEiView protein in PROSITE
PS00126 PDEASE_I_1, 1 hit
PS51845 PDEASE_I_2, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.iShow all

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F1T0K3F1T0K3_HUMAN
Phosphodiesterase
PDE6A
779Annotation score:

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 dbSNP:rs750539462Ensembl.1
Natural variantiVAR_025461102R → S in RP43. 1 PublicationCorresponds to variant dbSNP:rs141252097EnsemblClinVar.1
Natural variantiVAR_047730145A → T. Corresponds to variant dbSNP:rs35431421Ensembl.1
Natural variantiVAR_025462216N → S1 PublicationCorresponds to variant dbSNP:rs10057110EnsemblClinVar.1
Natural variantiVAR_025463277V → A1 PublicationCorresponds to variant dbSNP:rs145608358EnsemblClinVar.1
Natural variantiVAR_025464293P → L1 PublicationCorresponds to variant dbSNP:rs114973968EnsemblClinVar.1
Natural variantiVAR_006049344S → R in RP43. 1 PublicationCorresponds to variant dbSNP:rs121918577EnsemblClinVar.1
Natural variantiVAR_025465391V → M1 PublicationCorresponds to variant dbSNP:rs61732059EnsemblClinVar.1
Natural variantiVAR_047731492Q → H. Corresponds to variant dbSNP:rs17711594EnsemblClinVar.1
Natural variantiVAR_025466569Q → K in RP43. 1 PublicationCorresponds to variant dbSNP:rs139444207EnsemblClinVar.1
Natural variantiVAR_025467573S → P in RP43. 1 PublicationCorresponds to variant dbSNP:rs755527251Ensembl.1
Natural variantiVAR_025468827K → Q1 PublicationCorresponds to variant dbSNP:rs780450680Ensembl.1
Natural variantiVAR_025469850G → V1 PublicationCorresponds to variant dbSNP:rs138315990EnsemblClinVar.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

Similar proteinsi

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

PaxDbiP16499
PeptideAtlasiP16499
PRIDEiP16499
ProteomicsDBi53376

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi5145
DisGeNETi5145
EuPathDBiHostDB:ENSG00000132915.10
GeneCardsiPDE6A
GeneReviewsiPDE6A
HGNCiHGNC:8785 PDE6A
HPAiHPA016970
HPA074677
MalaCardsiPDE6A
MIMi180071 gene
613810 phenotype
neXtProtiNX_P16499
OpenTargetsiENSG00000132915
Orphaneti791 Retinitis pigmentosa
PharmGKBiPA33133
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3689 Eukaryota
ENOG410XRI7 LUCA
GeneTreeiENSGT00760000119066
HOGENOMiHOG000007069
HOVERGENiHBG053539
KOiK08718
OMAiLICNIMN
OrthoDBiEOG091G01RK
PhylomeDBiP16499
TreeFamiTF316499

Enzyme and pathway databases

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-CutDBiP16499
PROiPR:P16499
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000132915 Expressed in 56 organ(s), highest expression level in retina
CleanExiHS_PDE6A
ExpressionAtlasiP16499 baseline and differential
GenevisibleiP16499 HS

Family and domain databases

CDDicd00077 HDc, 1 hit
Gene3Di1.10.1300.10, 1 hit
3.30.450.40, 2 hits
InterProiView protein in InterPro
IPR003018 GAF
IPR029016 GAF-like_dom_sf
IPR003607 HD/PDEase_dom
IPR032958 PDE6A
IPR023088 PDEase
IPR002073 PDEase_catalytic_dom
IPR036971 PDEase_catalytic_dom_sf
IPR023174 PDEase_CS
PANTHERiPTHR11347:SF115 PTHR11347:SF115, 1 hit
PfamiView protein in Pfam
PF01590 GAF, 2 hits
PF00233 PDEase_I, 1 hit
PRINTSiPR00387 PDIESTERASE1
SMARTiView protein in SMART
SM00065 GAF, 2 hits
SM00471 HDc, 1 hit
PROSITEiView protein in PROSITE
PS00126 PDEASE_I_1, 1 hit
PS51845 PDEASE_I_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPDE6A_HUMAN
AccessioniPrimary (citable) accession number: P16499
Secondary accession number(s): Q0P638
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: November 25, 2008
Last modified: September 12, 2018
This is version 179 of the entry and version 4 of the sequence. See 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
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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