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Protein

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

Gene

PDE6B

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. Necessary for the formation of a functional phosphodiesterase holoenzyme.

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 sitei557Proton donorBy similarity1
Metal bindingi561Divalent metal cation 1By similarity1
Metal bindingi597Divalent metal cation 1By similarity1
Metal bindingi598Divalent metal cation 1By similarity1
Metal bindingi598Divalent metal cation 2By similarity1
Metal bindingi718Divalent 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
  • phototransduction, visible light Source: ProtInc
  • regulation of cytosolic calcium ion concentration Source: BHF-UCL
  • regulation of rhodopsin mediated signaling pathway Source: Reactome
  • retina development in camera-type eye Source: Ensembl
  • 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:ENSG00000133256-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 beta (EC:3.1.4.35)
Short name:
GMP-PDE beta
Gene namesi
Name:PDE6B
Synonyms:PDEB
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:8786. PDE6B.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Involvement in diseasei

Retinitis pigmentosa 40 (RP40)7 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:613801
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00928374R → C in RP40; autosomal recessive. Corresponds to variant rs144590560dbSNPEnsembl.1
Natural variantiVAR_068361100R → H in RP40. 1 PublicationCorresponds to variant rs555600300dbSNPEnsembl.1
Natural variantiVAR_009286219Y → H in RP40; autosomal recessive. Corresponds to variant rs62295357dbSNPEnsembl.1
Natural variantiVAR_009287228L → H in RP40; autosomal recessive and autosomal dominant. 1 Publication1
Natural variantiVAR_009290527L → P in RP40; autosomal recessive. Corresponds to variant rs760766981dbSNPEnsembl.1
Natural variantiVAR_009291535I → N in RP40; autosomal recessive. 1 PublicationCorresponds to variant rs527236088dbSNPEnsembl.1
Natural variantiVAR_009292552R → Q in RP40; autosomal recessive. 1 PublicationCorresponds to variant rs751859807dbSNPEnsembl.1
Natural variantiVAR_006050557H → Y in RP40; autosomal dominant. 1 PublicationCorresponds to variant rs121918581dbSNPEnsembl.1
Natural variantiVAR_006051576G → D in RP40; autosomal recessive. 1 Publication1
Natural variantiVAR_006052699L → R in RP40; autosomal recessive. 1 Publication1
Natural variantiVAR_068362776D → N in RP40. 1 PublicationCorresponds to variant rs141563823dbSNPEnsembl.1
Natural variantiVAR_009293854L → R in RP40; autosomal recessive. 1
Night blindness, congenital stationary, autosomal dominant 2 (CSNBAD2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia.
See also OMIM:163500
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_009289258H → N in CSNBAD2. 1 PublicationCorresponds to variant rs121918582dbSNPEnsembl.1

Keywords - Diseasei

Congenital stationary night blindness, Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi5158.
MalaCardsiPDE6B.
MIMi163500. phenotype.
613801. phenotype.
OpenTargetsiENSG00000133256.
Orphaneti215. Congenital stationary night blindness.
791. Retinitis pigmentosa.
PharmGKBiPA33134.

Chemistry databases

ChEMBLiCHEMBL2363066.
DrugBankiDB00201. Caffeine.

Polymorphism and mutation databases

BioMutaiPDE6B.
DMDMi226693550.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000233482 – 851Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit betaAdd BLAST850
PropeptideiPRO_0000023349852 – 854Removed in mature formBy similarity3

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi851S-geranylgeranyl cysteineBy similarity1

Keywords - PTMi

Lipoprotein, Prenylation

Proteomic databases

PaxDbiP35913.
PeptideAtlasiP35913.
PRIDEiP35913.

PTM databases

iPTMnetiP35913.
PhosphoSitePlusiP35913.

Expressioni

Gene expression databases

BgeeiENSG00000133256.
CleanExiHS_PDE6B.
ExpressionAtlasiP35913. baseline and differential.
GenevisibleiP35913. HS.

Organism-specific databases

HPAiHPA059929.

Interactioni

Subunit structurei

Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain.

Protein-protein interaction databases

BioGridi111184. 1 interactor.
STRINGi9606.ENSP00000420295.

Chemistry databases

BindingDBiP35913.

Structurei

3D structure databases

ProteinModelPortaliP35913.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini71 – 220GAF 1Add BLAST150
Domaini252 – 429GAF 2Add BLAST178

Sequence similaritiesi

Contains 2 GAF domains.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3689. Eukaryota.
ENOG410XRI7. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
KOiK13756.
OMAiSWVEYLS.
OrthoDBiEOG091G01RK.
PhylomeDBiP35913.
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]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P35913-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSLSEEQARS FLDQNPDFAR QYFGKKLSPE NVAAACEDGC PPDCDSLRDL
60 70 80 90 100
CQVEESTALL ELVQDMQESI NMERVVFKVL RRLCTLLQAD RCSLFMYRQR
110 120 130 140 150
NGVAELATRL FSVQPDSVLE DCLVPPDSEI VFPLDIGVVG HVAQTKKMVN
160 170 180 190 200
VEDVAECPHF SSFADELTDY KTKNMLATPI MNGKDVVAVI MAVNKLNGPF
210 220 230 240 250
FTSEDEDVFL KYLNFATLYL KIYHLSYLHN CETRRGQVLL WSANKVFEEL
260 270 280 290 300
TDIERQFHKA FYTVRAYLNC ERYSVGLLDM TKEKEFFDVW SVLMGESQPY
310 320 330 340 350
SGPRTPDGRE IVFYKVIDYV LHGKEEIKVI PTPSADHWAL ASGLPSYVAE
360 370 380 390 400
SGFICNIMNA SADEMFKFQE GALDDSGWLI KNVLSMPIVN KKEEIVGVAT
410 420 430 440 450
FYNRKDGKPF DEQDEVLMES LTQFLGWSVM NTDTYDKMNK LENRKDIAQD
460 470 480 490 500
MVLYHVKCDR DEIQLILPTR ARLGKEPADC DEDELGEILK EELPGPTTFD
510 520 530 540 550
IYEFHFSDLE CTELDLVKCG IQMYYELGVV RKFQIPQEVL VRFLFSISKG
560 570 580 590 600
YRRITYHNWR HGFNVAQTMF TLLMTGKLKS YYTDLEAFAM VTAGLCHDID
610 620 630 640 650
HRGTNNLYQM KSQNPLAKLH GSSILERHHL EFGKFLLSEE TLNIYQNLNR
660 670 680 690 700
RQHEHVIHLM DIAIIATDLA LYFKKRAMFQ KIVDESKNYQ DKKSWVEYLS
710 720 730 740 750
LETTRKEIVM AMMMTACDLS AITKPWEVQS KVALLVAAEF WEQGDLERTV
760 770 780 790 800
LDQQPIPMMD RNKAAELPKL QVGFIDFVCT FVYKEFSRFH EEILPMFDRL
810 820 830 840 850
QNNRKEWKAL ADEYEAKVKA LEEKEEEERV AAKKVGTEIC NGGPAPKSST

CCIL
Length:854
Mass (Da):98,336
Last modified:April 14, 2009 - v2
Checksum:iBB11A519BE88C9DF
GO
Isoform 2 (identifier: P35913-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     835-835: Missing.

Show »
Length:853
Mass (Da):98,237
Checksum:i1EE848D6E7BAB8BE
GO
Isoform 3 (identifier: P35913-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-279: Missing.

Note: No experimental confirmation available.
Show »
Length:575
Mass (Da):66,494
Checksum:i9A1DDC1F0956A149
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti33 – 35AAA → GRG in CAA44569 (PubMed:1720239).Curated3
Sequence conflicti33 – 35AAA → GRG in CAA46932 (PubMed:1338685).Curated3
Sequence conflicti33 – 35AAA → GRG in AAB22690 (PubMed:1322354).Curated3
Sequence conflicti315K → Q in CAA44569 (PubMed:1720239).Curated1
Sequence conflicti320V → L in CAA44569 (PubMed:1720239).Curated1
Sequence conflicti360A → R in CAA44569 (PubMed:1720239).Curated1
Sequence conflicti698Y → I in CAA44569 (PubMed:1720239).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00928374R → C in RP40; autosomal recessive. Corresponds to variant rs144590560dbSNPEnsembl.1
Natural variantiVAR_068361100R → H in RP40. 1 PublicationCorresponds to variant rs555600300dbSNPEnsembl.1
Natural variantiVAR_009284166E → K.1 PublicationCorresponds to variant rs115775983dbSNPEnsembl.1
Natural variantiVAR_009285212Y → H.1 PublicationCorresponds to variant rs551545798dbSNPEnsembl.1
Natural variantiVAR_009286219Y → H in RP40; autosomal recessive. Corresponds to variant rs62295357dbSNPEnsembl.1
Natural variantiVAR_009287228L → H in RP40; autosomal recessive and autosomal dominant. 1 Publication1
Natural variantiVAR_009288228L → I.Corresponds to variant rs201584824dbSNPEnsembl.1
Natural variantiVAR_009289258H → N in CSNBAD2. 1 PublicationCorresponds to variant rs121918582dbSNPEnsembl.1
Natural variantiVAR_054868320V → I.6 PublicationsCorresponds to variant rs10902758dbSNPEnsembl.1
Natural variantiVAR_009290527L → P in RP40; autosomal recessive. Corresponds to variant rs760766981dbSNPEnsembl.1
Natural variantiVAR_009291535I → N in RP40; autosomal recessive. 1 PublicationCorresponds to variant rs527236088dbSNPEnsembl.1
Natural variantiVAR_009292552R → Q in RP40; autosomal recessive. 1 PublicationCorresponds to variant rs751859807dbSNPEnsembl.1
Natural variantiVAR_006050557H → Y in RP40; autosomal dominant. 1 PublicationCorresponds to variant rs121918581dbSNPEnsembl.1
Natural variantiVAR_006051576G → D in RP40; autosomal recessive. 1 Publication1
Natural variantiVAR_054869654E → D.2 PublicationsCorresponds to variant rs17849286dbSNPEnsembl.1
Natural variantiVAR_006052699L → R in RP40; autosomal recessive. 1 Publication1
Natural variantiVAR_068362776D → N in RP40. 1 PublicationCorresponds to variant rs141563823dbSNPEnsembl.1
Natural variantiVAR_009293854L → R in RP40; autosomal recessive. 1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0449191 – 279Missing in isoform 3. 1 PublicationAdd BLAST279
Alternative sequenceiVSP_036884835Missing in isoform 2. 2 Publications1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X62692
, X62693, X62694, X62695 Genomic DNA. Translation: CAA44569.1.
X66142 mRNA. Translation: CAA46932.1.
S41458 mRNA. Translation: AAB22690.1.
BT009794 mRNA. Translation: AAP88796.1.
AK316054 mRNA. Translation: BAH14425.1.
AC107464 Genomic DNA. No translation available.
BC000249 mRNA. Translation: AAH00249.1.
X90587
, X90588, X90589, X90590 Genomic DNA. Translation: CAA62215.1.
CCDSiCCDS33932.1. [P35913-1]
CCDS46993.1. [P35913-3]
CCDS54703.1. [P35913-2]
PIRiA42828.
RefSeqiNP_000274.2. NM_000283.3.
NP_001138763.1. NM_001145291.1.
NP_001138764.1. NM_001145292.1.
XP_016863774.1. XM_017008285.1. [P35913-3]
XP_016863775.1. XM_017008286.1. [P35913-3]
UniGeneiHs.623810.
Hs.654544.

Genome annotation databases

EnsembliENST00000255622; ENSP00000255622; ENSG00000133256. [P35913-2]
ENST00000429163; ENSP00000406334; ENSG00000133256. [P35913-3]
ENST00000496514; ENSP00000420295; ENSG00000133256. [P35913-1]
GeneIDi5158.
KEGGihsa:5158.
UCSCiuc003gao.5. human. [P35913-1]

Keywords - Coding sequence diversityi

Alternative splicing, 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
X62692
, X62693, X62694, X62695 Genomic DNA. Translation: CAA44569.1.
X66142 mRNA. Translation: CAA46932.1.
S41458 mRNA. Translation: AAB22690.1.
BT009794 mRNA. Translation: AAP88796.1.
AK316054 mRNA. Translation: BAH14425.1.
AC107464 Genomic DNA. No translation available.
BC000249 mRNA. Translation: AAH00249.1.
X90587
, X90588, X90589, X90590 Genomic DNA. Translation: CAA62215.1.
CCDSiCCDS33932.1. [P35913-1]
CCDS46993.1. [P35913-3]
CCDS54703.1. [P35913-2]
PIRiA42828.
RefSeqiNP_000274.2. NM_000283.3.
NP_001138763.1. NM_001145291.1.
NP_001138764.1. NM_001145292.1.
XP_016863774.1. XM_017008285.1. [P35913-3]
XP_016863775.1. XM_017008286.1. [P35913-3]
UniGeneiHs.623810.
Hs.654544.

3D structure databases

ProteinModelPortaliP35913.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111184. 1 interactor.
STRINGi9606.ENSP00000420295.

Chemistry databases

BindingDBiP35913.
ChEMBLiCHEMBL2363066.
DrugBankiDB00201. Caffeine.

PTM databases

iPTMnetiP35913.
PhosphoSitePlusiP35913.

Polymorphism and mutation databases

BioMutaiPDE6B.
DMDMi226693550.

Proteomic databases

PaxDbiP35913.
PeptideAtlasiP35913.
PRIDEiP35913.

Protocols and materials databases

DNASUi5158.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000255622; ENSP00000255622; ENSG00000133256. [P35913-2]
ENST00000429163; ENSP00000406334; ENSG00000133256. [P35913-3]
ENST00000496514; ENSP00000420295; ENSG00000133256. [P35913-1]
GeneIDi5158.
KEGGihsa:5158.
UCSCiuc003gao.5. human. [P35913-1]

Organism-specific databases

CTDi5158.
DisGeNETi5158.
GeneCardsiPDE6B.
GeneReviewsiPDE6B.
H-InvDBHIX0031458.
HIX0031649.
HGNCiHGNC:8786. PDE6B.
HPAiHPA059929.
MalaCardsiPDE6B.
MIMi163500. phenotype.
180072. gene.
613801. phenotype.
neXtProtiNX_P35913.
OpenTargetsiENSG00000133256.
Orphaneti215. Congenital stationary night blindness.
791. Retinitis pigmentosa.
PharmGKBiPA33134.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3689. Eukaryota.
ENOG410XRI7. LUCA.
GeneTreeiENSGT00760000119066.
HOGENOMiHOG000007069.
HOVERGENiHBG053539.
KOiK13756.
OMAiSWVEYLS.
OrthoDBiEOG091G01RK.
PhylomeDBiP35913.
TreeFamiTF316499.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000133256-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

ChiTaRSiPDE6B. human.
GeneWikiiPDE6B.
GenomeRNAii5158.
PROiP35913.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000133256.
CleanExiHS_PDE6B.
ExpressionAtlasiP35913. baseline and differential.
GenevisibleiP35913. 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 nameiPDE6B_HUMAN
AccessioniPrimary (citable) accession number: P35913
Secondary accession number(s): B7Z9T9
, E7ETT3, Q53XN5, Q9BWH5, Q9UD49
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: April 14, 2009
Last modified: November 2, 2016
This is version 174 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: 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.