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P51160

- PDE6C_HUMAN

UniProt

P51160 - PDE6C_HUMAN

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Protein

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

Gene
PDE6C, PDEA2
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

Guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.

Cofactori

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
Binding sitei97 – 971cGMP By similarity
Binding sitei116 – 1161cGMP By similarity
Binding sitei176 – 1761cGMP By similarity
Active sitei562 – 5621Proton donor By similarity
Metal bindingi566 – 5661Divalent metal cation 1 By similarity
Metal bindingi602 – 6021Divalent metal cation 1 By similarity
Metal bindingi603 – 6031Divalent metal cation 1 By similarity
Metal bindingi603 – 6031Divalent metal cation 2 By similarity
Metal bindingi723 – 7231Divalent metal cation 1 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi169 – 1724cGMP By similarity

GO - Molecular functioni

  1. 3',5'-cyclic-GMP phosphodiesterase activity Source: UniProtKB-EC
  2. cGMP binding Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. phototransduction, visible light Source: Ensembl
  2. retinal cone cell development Source: Ensembl
  3. 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

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
ProteomesiUP000005640: Chromosome 10

Organism-specific databases

HGNCiHGNC:8787. PDE6C.

Subcellular locationi

GO - Cellular componenti

  1. plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Involvement in diseasei

Cone dystrophy 4 (COD4) [MIM:613093]: An 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.
Note: The disease is caused by mutations affecting the gene represented in this entry.1 Publication
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti29 – 291R → W in COD4. 1 Publication
VAR_062408
Natural varianti323 – 3231Y → N in COD4. 1 Publication
VAR_062409
Natural varianti455 – 4551M → V in COD4. 1 Publication
VAR_062410

Keywords - Diseasei

Disease mutation

Organism-specific databases

MIMi613093. phenotype.
Orphaneti49382. Achromatopsia.
1871. Progressive cone dystrophy.
PharmGKBiPA33135.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 855855Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'PRO_0000198831Add
BLAST
Propeptidei856 – 8583Removed in mature form Reviewed predictionPRO_0000370788

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei855 – 8551Cysteine methyl ester Reviewed prediction
Lipidationi855 – 8551S-geranylgeranyl cysteine By similarity

Keywords - PTMi

Lipoprotein, Methylation, Prenylation

Proteomic databases

PaxDbiP51160.
PRIDEiP51160.

PTM databases

PhosphoSiteiP51160.

Expressioni

Gene expression databases

BgeeiP51160.
CleanExiHS_PDE6C.
GenevestigatoriP51160.

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.

Structurei

Secondary structure

1
858
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi746 – 7549
Helixi762 – 7643
Helixi766 – 7716
Helixi772 – 78211

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3JWQX-ray2.87A/B/C/D746-785[»]
3JWRX-ray2.99A/B746-785[»]
ProteinModelPortaliP51160.
SMRiP51160. Positions 24-820.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini75 – 224150GAF 1Add
BLAST
Domaini256 – 433178GAF 2Add
BLAST

Sequence similaritiesi

Contains 2 GAF domains.

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiNOG290744.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
InParanoidiP51160.
KOiK13757.
OMAiCGIRLFF.
OrthoDBiEOG7BGHK1.
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

MGEINQVAVE KYLEENPQFA KEYFDRKLRV EVLGEIFKNS QVPVQSSMSF    50
SELTQVEESA LCLELLWTVQ EEGGTPEQGV HRALQRLAHL LQADRCSMFL 100
CRSRNGIPEV ASRLLDVTPT SKFEDNLVGP DKEVVFPLDI GIVGWAAHTK 150
KTHNVPDVKK NSHFSDFMDK QTGYVTKNLL ATPIVVGKEV LAVIMAVNKV 200
NASEFSKQDE EVFSKYLNFV SIILRLHHTS YMYNIESRRS QILMWSANKV 250
FEELTDVERQ FHKALYTVRS YLNCERYSIG LLDMTKEKEF YDEWPIKLGE 300
VEPYKGPKTP DGREVNFYKI IDYILHGKEE IKVIPTPPAD HWTLISGLPT 350
YVAENGFICN MMNAPADEYF TFQKGPVDET GWVIKNVLSL PIVNKKEDIV 400
GVATFYNRKD GKPFDEHDEY ITETLTQFLG WSLLNTDTYD KMNKLENRKD 450
IAQEMLMNQT KATPEEIKSI LKFQEKLNVD VIDDCEEKQL VAILKEDLPD 500
PRSAELYEFR FSDFPLTEHG LIKCGIRLFF EINVVEKFKV PVEVLTRWMY 550
TVRKGYRAVT YHNWRHGFNV GQTMFTLLMT GRLKKYYTDL EAFAMLAAAF 600
CHDIDHRGTN NLYQMKSTSP LARLHGSSIL ERHHLEYSKT LLQDESLNIF 650
QNLNKRQFET VIHLFEVAII ATDLALYFKK RTMFQKIVDA CEQMQTEEEA 700
IKYVTVDPTK KEIIMAMMMT ACDLSAITKP WEVQSQVALM VANEFWEQGD 750
LERTVLQQQP IPMMDRNKRD ELPKLQVGFI DFVCTFVYKE FSRFHKEITP 800
MLSGLQNNRV EWKSLADEYD AKMKVIEEEA KKQEGGAEKA AEDSGGGDDK 850
KSKTCLML 858
Length:858
Mass (Da):99,147
Last modified:March 7, 2006 - v2
Checksum:i06FFD025EE5936A5
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti29 – 291R → W in COD4. 1 Publication
VAR_062408
Natural varianti157 – 1571D → E Rare polymorphism. 1 Publication
Corresponds to variant rs76999928 [ dbSNP | Ensembl ].
VAR_025470
Natural varianti270 – 2701S → T.1 Publication
Corresponds to variant rs701865 [ dbSNP | Ensembl ].
VAR_050475
Natural varianti323 – 3231Y → N in COD4. 1 Publication
VAR_062409
Natural varianti455 – 4551M → V in COD4. 1 Publication
VAR_062410
Natural varianti699 – 6991E → A.
Corresponds to variant rs12261131 [ dbSNP | Ensembl ].
VAR_050476
Natural varianti822 – 8221K → N Rare polymorphism. 1 Publication
Corresponds to variant rs79487435 [ dbSNP | Ensembl ].
VAR_025471
Natural varianti826 – 8261I → S Found in a renal cell carcinoma sample; somatic mutation. 1 Publication
VAR_064744
Natural varianti834 – 8341E → G Rare polymorphism. 1 Publication
VAR_025472

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti116 – 1161D → V in AAA96392. 1 Publication
Sequence conflicti116 – 1161D → V in AAA92886. 1 Publication
Sequence conflicti373 – 3731Q → P in AAA96392. 1 Publication
Sequence conflicti464 – 4641P → L in AAA96392. 1 Publication
Sequence conflicti565 – 5651R → Q in AAA96392. 1 Publication
Sequence conflicti565 – 5651R → Q in AAA92886. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.4. human.

Polymorphism databases

DMDMi90111861.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS7429.1.
PIRi S63688. JC4520.
RefSeqi NP_006195.3. NM_006204.3.
UniGenei Hs.658121.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3JWQ X-ray 2.87 A/B/C/D 746-785 [» ]
3JWR X-ray 2.99 A/B 746-785 [» ]
ProteinModelPortali P51160.
SMRi P51160. Positions 24-820.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 9606.ENSP00000360502.

Chemistry

BindingDBi P51160.
ChEMBLi CHEMBL2363066.

PTM databases

PhosphoSitei P51160.

Polymorphism databases

DMDMi 90111861.

Proteomic databases

PaxDbi P51160.
PRIDEi P51160.

Protocols and materials databases

DNASUi 5146.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000371447 ; ENSP00000360502 ; ENSG00000095464 .
GeneIDi 5146.
KEGGi hsa:5146.
UCSCi uc001kiu.4. human.

Organism-specific databases

CTDi 5146.
GeneCardsi GC10P095362.
GeneReviewsi PDE6C.
H-InvDB HIX0035433.
HGNCi HGNC:8787. PDE6C.
MIMi 600827. gene.
613093. phenotype.
neXtProti NX_P51160.
Orphaneti 49382. Achromatopsia.
1871. Progressive cone dystrophy.
PharmGKBi PA33135.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG290744.
HOGENOMi HOG000007069.
HOVERGENi HBG053539.
InParanoidi P51160.
KOi K13757.
OMAi CGIRLFF.
OrthoDBi EOG7BGHK1.
PhylomeDBi P51160.
TreeFami TF316499.

Miscellaneous databases

GeneWikii PDE6C.
GenomeRNAii 5146.
NextBioi 19856.
PROi P51160.
SOURCEi Search...

Gene expression databases

Bgeei P51160.
CleanExi HS_PDE6C.
Genevestigatori P51160.

Family and domain databases

Gene3Di 1.10.1300.10. 1 hit.
3.30.450.40. 3 hits.
InterProi IPR003018. GAF.
IPR029016. GAF_dom_like.
IPR003607. HD/PDEase_dom.
IPR023088. PDEase.
IPR002073. PDEase_catalytic_dom.
IPR023174. PDEase_CS.
[Graphical view ]
Pfami PF01590. GAF. 2 hits.
PF00233. PDEase_I. 1 hit.
[Graphical view ]
PRINTSi PR00387. PDIESTERASE1.
SMARTi SM00065. GAF. 2 hits.
SM00471. HDc. 1 hit.
[Graphical view ]
SUPFAMi SSF55781. SSF55781. 3 hits.
PROSITEi PS00126. PDEASE_I. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and characterization of a cDNA encoding the alpha' subunit of human cone cGMP-phosphodiesterase."
    Viczian A.S., Piriev N.I., Farber D.B.
    Gene 166:205-211(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Retina.
  2. "Gene structure and amino acid sequence of the human cone photoreceptor cGMP-phosphodiesterase alpha' subunit (PDEA2) and its chromosomal localization to 10q24."
    Piriev N.I., Viczian A.S., Ye J., Kerner B., Korenberg J.R., Farber D.B.
    Genomics 28:429-435(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Tissue: Retina.
  3. "Human cone-specific cGMP phosphodiesterase alpha' subunit: complete cDNA sequence and gene arrangement."
    Feshchenko E.A., Andreeva S.G., Suslova V.A., Smirnova E.V., Zagranichny V.E., Lipkin V.M.
    FEBS Lett. 381:149-152(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], VARIANT THR-270.
    Tissue: Retina.
  4. "The DNA sequence and comparative analysis of human chromosome 10."
    Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J.
    , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
    Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "Screening of the gene encoding the alpha'-subunit of cone cGMP-PDE in patients with retinal degenerations."
    Gao Y.Q., Danciger M., Longmuir R., Piriev N.I., Zhao D.Y., Heckenlively J.R., Fishman G.A., Weleber R.G., Jacobson S.G., Stone E.M., Farber D.B.
    Invest. Ophthalmol. Vis. Sci. 40:1818-1822(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS GLU-157; ASN-822 AND GLY-834.
  7. Cited for: VARIANTS COD4 TRP-29; ASN-323 AND VAL-455.
  8. Cited for: VARIANT SER-826.

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: September 3, 2014
This is version 135 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

External Data

Dasty 3

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