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Protein

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Gene

PDE6D

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

Functioni

Promotes the release of prenylated target proteins from cellular membranes (PubMed:9712853). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22002721, PubMed:23698361). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (PubMed:24166846). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (By similarity). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate (By similarity).By similarity6 Publications

GO - Molecular functioni

GO - Biological processi

  • response to stimulus Source: UniProtKB-KW
  • visual perception Source: ProtInc

Keywordsi

Biological processSensory transduction, Vision
LigandcGMP

Enzyme and pathway databases

ReactomeiR-HSA-5624958 ARL13B-mediated ciliary trafficking of INPP5E

Names & Taxonomyi

Protein namesi
Recommended name:
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Short name:
GMP-PDE delta
Alternative name(s):
Protein p17
Gene namesi
Name:PDE6D
Synonyms:PDED
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000156973.13
HGNCiHGNC:8788 PDE6D
MIMi602676 gene
neXtProtiNX_O43924

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 projection, Cytoplasm, Cytoplasmic vesicle, Cytoskeleton, Membrane

Pathology & Biotechi

Involvement in diseasei

Joubert syndrome 22 (JBTS22)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly.
See also OMIM:615665

Keywords - Diseasei

Ciliopathy, Joubert syndrome

Organism-specific databases

DisGeNETi5147
MalaCardsiPDE6D
MIMi615665 phenotype
OpenTargetsiENSG00000156973
Orphaneti2754 Joubert syndrome with orofaciodigital defect
PharmGKBiPA33136

Chemistry databases

ChEMBLiCHEMBL3860

Polymorphism and mutation databases

BioMutaiPDE6D

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002212081 – 150Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit deltaAdd BLAST150

Proteomic databases

EPDiO43924
PaxDbiO43924
PeptideAtlasiO43924
PRIDEiO43924
ProteomicsDBi49239

PTM databases

iPTMnetiO43924
PhosphoSitePlusiO43924

Expressioni

Tissue specificityi

Widely expressed. Detected in various tissues including spleen, prostate gland, testis, ovary, small intestine, colon, retina, and peripheral blood.1 Publication

Gene expression databases

BgeeiENSG00000156973 Expressed in 220 organ(s), highest expression level in C1 segment of cervical spinal cord
CleanExiHS_PDE6D
ExpressionAtlasiO43924 baseline and differential
GenevisibleiO43924 HS

Organism-specific databases

HPAiHPA037433
HPA037434

Interactioni

Subunit structurei

Interacts with the prenylated catalytic subunits of PDE6, an oligomer composed of two catalytic chains (PDE6A and PDE6B) and two inhibitory chains (gamma); has no effect on enzyme activity but promotes the release of the prenylated enzyme from cell membrane (By similarity). Interacts with prenylated GRK1 and GRK7 (By similarity). Interacts with prenylated Ras family members, including RAP2A and RAP2C (By similarity). Interacts with prenylated RHEB and NRAS (PubMed:22002721). Interacts with prenylated HRAS and KRAS. Interacts with RAB13 (prenylated form); dissociates RAB13 from membranes (PubMed:9712853). Interacts with prenylated INPP5E (PubMed:24166846). Interacts with RPGR (PubMed:9990021, PubMed:24166846, PubMed:23559067). Interacts with ARL2 (PubMed:24166846, PubMed:22002721). Interacts with ARL3; the interaction occurs specifically with the GTP-bound form of ARL3 (PubMed:24166846). Interaction with ARL2 and ARL3 promotes release of farnesylated cargo proteins (PubMed:22002721).By similarity7 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111173, 28 interactors
CORUMiO43924
DIPiDIP-36660N
IntActiO43924, 19 interactors
MINTiO43924
STRINGi9606.ENSP00000287600

Chemistry databases

BindingDBiO43924

Structurei

Secondary structure

1150
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO43924
SMRiO43924
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO43924

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni144 – 150Required for association with membranes1 Publication7

Sequence similaritiesi

Belongs to the PDE6D/unc-119 family.Curated

Phylogenomic databases

eggNOGiKOG4038 Eukaryota
ENOG4110ZMQ LUCA
GeneTreeiENSGT00390000000263
HOGENOMiHOG000007689
HOVERGENiHBG053542
KOiK13758
OMAiLWQGNED
OrthoDBiEOG091G0SV1
PhylomeDBiO43924
TreeFamiTF314474

Family and domain databases

Gene3Di2.70.50.40, 1 hit
InterProiView protein in InterPro
IPR014756 Ig_E-set
IPR008015 PDED_dom
IPR037036 PDED_dom_sf
IPR017287 Rhodop-sen_GMP-Pdiesterase_dsu
PfamiView protein in Pfam
PF05351 GMP_PDE_delta, 1 hit
PIRSFiPIRSF037825 GMP-Pdiesterase_delta, 1 hit
SUPFAMiSSF81296 SSF81296, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.iShow all

O43924-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSAKDERARE ILRGFKLNWM NLRDAETGKI LWQGTEDLSV PGVEHEARVP
60 70 80 90 100
KKILKCKAVS RELNFSSTEQ MEKFRLEQKV YFKGQCLEEW FFEFGFVIPN
110 120 130 140 150
STNTWQSLIE AAPESQMMPA SVLTGNVIIE TKFFDDDLLV STSRVRLFYV
Length:150
Mass (Da):17,420
Last modified:June 1, 1998 - v1
Checksum:iAB8D9309C33B4411
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B8ZZK5B8ZZK5_HUMAN
Phosphodiesterase 6D, cGMP-specific...
PDE6D hCG_32951
93Annotation score:
C9IZ52C9IZ52_HUMAN
Retinal rod rhodopsin-sensitive cGM...
PDE6D
104Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti117M → V in CAA04880 (PubMed:9712853).Curated1
Sequence conflicti146R → G in CAA04880 (PubMed:9712853).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF045999 Genomic DNA Translation: AAC39720.1
AF022912 mRNA Translation: AAB87872.1
AF042835, AF042833, AF042834 Genomic DNA Translation: AAC25953.1
AJ001626 mRNA Translation: CAA04880.1
BT007278 mRNA Translation: AAP35942.1
BC007831 mRNA Translation: AAH07831.1
CCDSiCCDS33398.1
RefSeqiNP_001277947.1, NM_001291018.1
NP_002592.1, NM_002601.3
UniGeneiHs.516808

Genome annotation databases

EnsembliENST00000287600; ENSP00000287600; ENSG00000156973
GeneIDi5147
KEGGihsa:5147

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF045999 Genomic DNA Translation: AAC39720.1
AF022912 mRNA Translation: AAB87872.1
AF042835, AF042833, AF042834 Genomic DNA Translation: AAC25953.1
AJ001626 mRNA Translation: CAA04880.1
BT007278 mRNA Translation: AAP35942.1
BC007831 mRNA Translation: AAH07831.1
CCDSiCCDS33398.1
RefSeqiNP_001277947.1, NM_001291018.1
NP_002592.1, NM_002601.3
UniGeneiHs.516808

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KSGX-ray2.30B1-150[»]
1KSHX-ray1.80B1-150[»]
1KSJX-ray2.60B1-150[»]
3T5GX-ray1.70B1-150[»]
3T5IX-ray2.10A/B/C/D1-150[»]
4JHPX-ray1.90B1-150[»]
4JV6X-ray1.87B1-150[»]
4JV8X-ray1.45B1-150[»]
4JVBX-ray1.75B1-150[»]
4JVFX-ray2.40B1-150[»]
5E80X-ray2.60A/B2-150[»]
5E8FX-ray2.10A/C2-150[»]
5F2UX-ray1.85A/B2-150[»]
5ML2X-ray1.60B2-150[»]
5ML3X-ray1.40B2-150[»]
5ML4X-ray2.40B2-150[»]
5ML6X-ray1.87B2-150[»]
5ML8X-ray2.60B2-150[»]
5NALX-ray2.20B1-150[»]
5TARX-ray1.90B3-150[»]
5TB5X-ray2.00B/D1-150[»]
5X72X-ray1.95A1-150[»]
5X73X-ray2.50A1-150[»]
5X74X-ray2.25A1-150[»]
ProteinModelPortaliO43924
SMRiO43924
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111173, 28 interactors
CORUMiO43924
DIPiDIP-36660N
IntActiO43924, 19 interactors
MINTiO43924
STRINGi9606.ENSP00000287600

Chemistry databases

BindingDBiO43924
ChEMBLiCHEMBL3860

PTM databases

iPTMnetiO43924
PhosphoSitePlusiO43924

Polymorphism and mutation databases

BioMutaiPDE6D

Proteomic databases

EPDiO43924
PaxDbiO43924
PeptideAtlasiO43924
PRIDEiO43924
ProteomicsDBi49239

Protocols and materials databases

DNASUi5147
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000287600; ENSP00000287600; ENSG00000156973
GeneIDi5147
KEGGihsa:5147

Organism-specific databases

CTDi5147
DisGeNETi5147
EuPathDBiHostDB:ENSG00000156973.13
GeneCardsiPDE6D
HGNCiHGNC:8788 PDE6D
HPAiHPA037433
HPA037434
MalaCardsiPDE6D
MIMi602676 gene
615665 phenotype
neXtProtiNX_O43924
OpenTargetsiENSG00000156973
Orphaneti2754 Joubert syndrome with orofaciodigital defect
PharmGKBiPA33136
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4038 Eukaryota
ENOG4110ZMQ LUCA
GeneTreeiENSGT00390000000263
HOGENOMiHOG000007689
HOVERGENiHBG053542
KOiK13758
OMAiLWQGNED
OrthoDBiEOG091G0SV1
PhylomeDBiO43924
TreeFamiTF314474

Enzyme and pathway databases

ReactomeiR-HSA-5624958 ARL13B-mediated ciliary trafficking of INPP5E

Miscellaneous databases

ChiTaRSiPDE6D human
EvolutionaryTraceiO43924
GeneWikiiPDE6D
GenomeRNAii5147
PROiPR:O43924
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000156973 Expressed in 220 organ(s), highest expression level in C1 segment of cervical spinal cord
CleanExiHS_PDE6D
ExpressionAtlasiO43924 baseline and differential
GenevisibleiO43924 HS

Family and domain databases

Gene3Di2.70.50.40, 1 hit
InterProiView protein in InterPro
IPR014756 Ig_E-set
IPR008015 PDED_dom
IPR037036 PDED_dom_sf
IPR017287 Rhodop-sen_GMP-Pdiesterase_dsu
PfamiView protein in Pfam
PF05351 GMP_PDE_delta, 1 hit
PIRSFiPIRSF037825 GMP-Pdiesterase_delta, 1 hit
SUPFAMiSSF81296 SSF81296, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPDE6D_HUMAN
AccessioniPrimary (citable) accession number: O43924
Secondary accession number(s): O43250
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: June 1, 1998
Last modified: September 12, 2018
This is version 166 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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