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Protein

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

Gene

PDE6C

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

Functioni

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
Binding sitei97cGMPBy similarity1
Binding sitei116cGMPBy similarity1
Binding sitei176cGMPBy similarity1
Active sitei562Proton donorBy similarity1
Metal bindingi566Divalent metal cation 1By similarity1
Metal bindingi602Divalent metal cation 1By similarity1
Metal bindingi603Divalent metal cation 1By similarity1
Metal bindingi603Divalent metal cation 2By similarity1
Metal bindingi723Divalent metal cation 1By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi169 – 172cGMPBy similarity4

GO - Molecular functioni

GO - Biological processi

  • phototransduction, visible light Source: Ensembl
  • retinal cone cell development Source: Ensembl
  • visual perception Source: ProtInc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Sensory transduction, Vision

Keywords - Ligandi

cGMP, cGMP-binding, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:HS01821-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' (EC:3.1.4.35)
Alternative name(s):
cGMP phosphodiesterase 6C
Gene namesi
Name:PDE6C
Synonyms:PDEA2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:8787. PDE6C.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Involvement in diseasei

Cone dystrophy 4 (COD4)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn early-onset cone dystrophy. Cone dystrophies are retinal dystrophies characterized by progressive degeneration of the cone photoreceptors with preservation of rod function, as indicated by electroretinogram. However, some rod involvement may be present in some cone dystrophies, particularly at late stage. Affected individuals suffer from photophobia, loss of visual acuity, color vision and central visual field. Another sign is the absence of macular lesions for many years. Cone dystrophies are distinguished from the cone-rod dystrophies in which some loss of peripheral vision also occurs.
See also OMIM:613093
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06240829R → W in COD4. 1 PublicationCorresponds to variant rs121918537dbSNPEnsembl.1
Natural variantiVAR_062409323Y → N in COD4. 1 PublicationCorresponds to variant rs121918538dbSNPEnsembl.1
Natural variantiVAR_062410455M → V in COD4. 1 PublicationCorresponds to variant rs121918539dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi5146.
MalaCardsiPDE6C.
MIMi613093. phenotype.
OpenTargetsiENSG00000095464.
Orphaneti49382. Achromatopsia.
1871. Progressive cone dystrophy.
PharmGKBiPA33135.

Chemistry databases

ChEMBLiCHEMBL3977.
DrugBankiDB00201. Caffeine.
GuidetoPHARMACOLOGYi1314.

Polymorphism and mutation databases

BioMutaiPDE6C.
DMDMi90111861.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001988311 – 855Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'Add BLAST855
PropeptideiPRO_0000370788856 – 858Removed in mature formSequence analysis3

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei855Cysteine methyl esterSequence analysis1
Lipidationi855S-geranylgeranyl cysteineBy similarity1

Keywords - PTMi

Lipoprotein, Methylation, Prenylation

Proteomic databases

EPDiP51160.
PaxDbiP51160.
PeptideAtlasiP51160.
PRIDEiP51160.

PTM databases

iPTMnetiP51160.
PhosphoSitePlusiP51160.

Expressioni

Gene expression databases

BgeeiENSG00000095464.
CleanExiHS_PDE6C.
GenevisibleiP51160. HS.

Organism-specific databases

HPAiCAB009333.
CAB016291.

Interactioni

Subunit structurei

Composed of two alpha' subunits that are associated with 3 smaller proteins of 11, 13, and 15 kDa.

Protein-protein interaction databases

STRINGi9606.ENSP00000360502.

Chemistry databases

BindingDBiP51160.

Structurei

Secondary structure

1858
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi746 – 754Combined sources9
Helixi762 – 764Combined sources3
Helixi766 – 771Combined sources6
Helixi772 – 782Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JWQX-ray2.87A/B/C/D746-785[»]
3JWRX-ray2.99A/B746-785[»]
5E8FX-ray2.10D/E851-855[»]
ProteinModelPortaliP51160.
SMRiP51160.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini75 – 224GAF 1Add BLAST150
Domaini256 – 433GAF 2Add BLAST178

Sequence similaritiesi

Contains 2 GAF domains.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3689. Eukaryota.
ENOG410XRI7. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
KOiK13757.
OMAiIVMGKEV.
OrthoDBiEOG091G01RK.
PhylomeDBiP51160.
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.

P51160-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGEINQVAVE KYLEENPQFA KEYFDRKLRV EVLGEIFKNS QVPVQSSMSF
60 70 80 90 100
SELTQVEESA LCLELLWTVQ EEGGTPEQGV HRALQRLAHL LQADRCSMFL
110 120 130 140 150
CRSRNGIPEV ASRLLDVTPT SKFEDNLVGP DKEVVFPLDI GIVGWAAHTK
160 170 180 190 200
KTHNVPDVKK NSHFSDFMDK QTGYVTKNLL ATPIVVGKEV LAVIMAVNKV
210 220 230 240 250
NASEFSKQDE EVFSKYLNFV SIILRLHHTS YMYNIESRRS QILMWSANKV
260 270 280 290 300
FEELTDVERQ FHKALYTVRS YLNCERYSIG LLDMTKEKEF YDEWPIKLGE
310 320 330 340 350
VEPYKGPKTP DGREVNFYKI IDYILHGKEE IKVIPTPPAD HWTLISGLPT
360 370 380 390 400
YVAENGFICN MMNAPADEYF TFQKGPVDET GWVIKNVLSL PIVNKKEDIV
410 420 430 440 450
GVATFYNRKD GKPFDEHDEY ITETLTQFLG WSLLNTDTYD KMNKLENRKD
460 470 480 490 500
IAQEMLMNQT KATPEEIKSI LKFQEKLNVD VIDDCEEKQL VAILKEDLPD
510 520 530 540 550
PRSAELYEFR FSDFPLTEHG LIKCGIRLFF EINVVEKFKV PVEVLTRWMY
560 570 580 590 600
TVRKGYRAVT YHNWRHGFNV GQTMFTLLMT GRLKKYYTDL EAFAMLAAAF
610 620 630 640 650
CHDIDHRGTN NLYQMKSTSP LARLHGSSIL ERHHLEYSKT LLQDESLNIF
660 670 680 690 700
QNLNKRQFET VIHLFEVAII ATDLALYFKK RTMFQKIVDA CEQMQTEEEA
710 720 730 740 750
IKYVTVDPTK KEIIMAMMMT ACDLSAITKP WEVQSQVALM VANEFWEQGD
760 770 780 790 800
LERTVLQQQP IPMMDRNKRD ELPKLQVGFI DFVCTFVYKE FSRFHKEITP
810 820 830 840 850
MLSGLQNNRV EWKSLADEYD AKMKVIEEEA KKQEGGAEKA AEDSGGGDDK

KSKTCLML
Length:858
Mass (Da):99,147
Last modified:March 7, 2006 - v2
Checksum:i06FFD025EE5936A5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti116D → V in AAA96392 (PubMed:8543163).Curated1
Sequence conflicti116D → V in AAA92886 (PubMed:7490077).Curated1
Sequence conflicti373Q → P in AAA96392 (PubMed:8543163).Curated1
Sequence conflicti464P → L in AAA96392 (PubMed:8543163).Curated1
Sequence conflicti565R → Q in AAA96392 (PubMed:8543163).Curated1
Sequence conflicti565R → Q in AAA92886 (PubMed:7490077).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06240829R → W in COD4. 1 PublicationCorresponds to variant rs121918537dbSNPEnsembl.1
Natural variantiVAR_025470157D → E Rare polymorphism. 1 PublicationCorresponds to variant rs76999928dbSNPEnsembl.1
Natural variantiVAR_050475270S → T.1 PublicationCorresponds to variant rs701865dbSNPEnsembl.1
Natural variantiVAR_062409323Y → N in COD4. 1 PublicationCorresponds to variant rs121918538dbSNPEnsembl.1
Natural variantiVAR_062410455M → V in COD4. 1 PublicationCorresponds to variant rs121918539dbSNPEnsembl.1
Natural variantiVAR_050476699E → A.Corresponds to variant rs12261131dbSNPEnsembl.1
Natural variantiVAR_025471822K → N Rare polymorphism. 1 PublicationCorresponds to variant rs79487435dbSNPEnsembl.1
Natural variantiVAR_064744826I → S Found in a renal cell carcinoma sample; somatic mutation. 1 Publication1
Natural variantiVAR_025472834E → G Rare polymorphism. 1 PublicationCorresponds to variant rs148661165dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31973 mRNA. Translation: AAA96392.1.
U20212
, U20196, U20197, U20199, U20200, U20201, U20202, U20203, U20204, U20205, U20206, U20207, U20208, U20209, U20210, U20211 Genomic DNA. Translation: AAA92886.1.
X94354 Genomic DNA. Translation: CAA64079.1.
AL356214, AL157396 Genomic DNA. Translation: CAH72330.1.
AL157396, AL356214 Genomic DNA. Translation: CAH73839.1.
CH471066 Genomic DNA. Translation: EAW50064.1.
CCDSiCCDS7429.1.
PIRiS63688. JC4520.
RefSeqiNP_006195.3. NM_006204.3.
UniGeneiHs.658121.

Genome annotation databases

EnsembliENST00000371447; ENSP00000360502; ENSG00000095464.
GeneIDi5146.
KEGGihsa:5146.
UCSCiuc001kiu.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31973 mRNA. Translation: AAA96392.1.
U20212
, U20196, U20197, U20199, U20200, U20201, U20202, U20203, U20204, U20205, U20206, U20207, U20208, U20209, U20210, U20211 Genomic DNA. Translation: AAA92886.1.
X94354 Genomic DNA. Translation: CAA64079.1.
AL356214, AL157396 Genomic DNA. Translation: CAH72330.1.
AL157396, AL356214 Genomic DNA. Translation: CAH73839.1.
CH471066 Genomic DNA. Translation: EAW50064.1.
CCDSiCCDS7429.1.
PIRiS63688. JC4520.
RefSeqiNP_006195.3. NM_006204.3.
UniGeneiHs.658121.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JWQX-ray2.87A/B/C/D746-785[»]
3JWRX-ray2.99A/B746-785[»]
5E8FX-ray2.10D/E851-855[»]
ProteinModelPortaliP51160.
SMRiP51160.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000360502.

Chemistry databases

BindingDBiP51160.
ChEMBLiCHEMBL3977.
DrugBankiDB00201. Caffeine.
GuidetoPHARMACOLOGYi1314.

PTM databases

iPTMnetiP51160.
PhosphoSitePlusiP51160.

Polymorphism and mutation databases

BioMutaiPDE6C.
DMDMi90111861.

Proteomic databases

EPDiP51160.
PaxDbiP51160.
PeptideAtlasiP51160.
PRIDEiP51160.

Protocols and materials databases

DNASUi5146.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000371447; ENSP00000360502; ENSG00000095464.
GeneIDi5146.
KEGGihsa:5146.
UCSCiuc001kiu.5. human.

Organism-specific databases

CTDi5146.
DisGeNETi5146.
GeneCardsiPDE6C.
GeneReviewsiPDE6C.
H-InvDBHIX0035433.
HGNCiHGNC:8787. PDE6C.
HPAiCAB009333.
CAB016291.
MalaCardsiPDE6C.
MIMi600827. gene.
613093. phenotype.
neXtProtiNX_P51160.
OpenTargetsiENSG00000095464.
Orphaneti49382. Achromatopsia.
1871. Progressive cone dystrophy.
PharmGKBiPA33135.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3689. Eukaryota.
ENOG410XRI7. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
KOiK13757.
OMAiIVMGKEV.
OrthoDBiEOG091G01RK.
PhylomeDBiP51160.
TreeFamiTF316499.

Enzyme and pathway databases

BioCyciZFISH:HS01821-MONOMER.

Miscellaneous databases

GeneWikiiPDE6C.
GenomeRNAii5146.
PROiP51160.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000095464.
CleanExiHS_PDE6C.
GenevisibleiP51160. 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.
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...

Entry informationi

Entry nameiPDE6C_HUMAN
AccessioniPrimary (citable) accession number: P51160
Secondary accession number(s): A6NCR6, Q5VY29
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: March 7, 2006
Last modified: November 2, 2016
This is version 158 of the entry and version 2 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.