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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: Annotation score: 5 out of 5-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
Complete GO annotation...

Keywords - Biological processi

Sensory transduction, Vision

Keywords - Ligandi

cGMP

Enzyme and pathway databases

BioCyciZFISH:ENSG00000156973-MONOMER.
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

HGNCiHGNC:8788. PDE6D.

Subcellular locationi

GO - Cellular componenti

  • cell projection Source: UniProtKB-KW
  • cytoplasmic vesicle Source: UniProtKB
  • cytoplasmic vesicle membrane Source: UniProtKB-SubCell
  • cytoskeleton Source: UniProtKB-KW
  • cytosol Source: UniProtKB
Complete GO annotation...

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.

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.
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

WithEntry#Exp.IntActNotes
ARL16Q0P5N69EBI-712685,EBI-10186132
ARL2P3640414EBI-712685,EBI-752365
Arl2Q9D0J46EBI-712685,EBI-1033319From a different organism.
ARL3P364054EBI-712685,EBI-712710
Arl3Q9WUL74EBI-712685,EBI-6860857From a different organism.
RAB13P511532EBI-712685,EBI-1780121
RHEBQ153825EBI-712685,EBI-6860739
RPGRQ928349EBI-712685,EBI-6558417
tirQ7DB773EBI-712685,EBI-6480811From a different organism.

GO - Molecular functioni

  • Rab GTPase binding Source: UniProtKB

Protein-protein interaction databases

BioGridi111173. 26 interactors.
DIPiDIP-36660N.
IntActiO43924. 17 interactors.
MINTiMINT-236371.
STRINGi9606.ENSP00000287600.

Chemistry databases

BindingDBiO43924.

Structurei

Secondary structure

1150
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 13Combined sources11
Beta strandi15 – 24Combined sources10
Turni25 – 27Combined sources3
Beta strandi30 – 34Combined sources5
Beta strandi43 – 50Combined sources8
Helixi51 – 55Combined sources5
Beta strandi57 – 69Combined sources13
Beta strandi71 – 82Combined sources12
Beta strandi85 – 97Combined sources13
Beta strandi101 – 110Combined sources10
Helixi114 – 116Combined sources3
Helixi120 – 123Combined sources4
Turni124 – 126Combined sources3
Beta strandi127 – 135Combined sources9
Beta strandi138 – 150Combined sources13

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[»]
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.
OMAiSTNTWQN.
OrthoDBiEOG091G0SV1.
PhylomeDBiO43924.
TreeFamiTF314474.

Family and domain databases

Gene3Di2.70.50.40. 1 hit.
InterProiIPR014756. Ig_E-set.
IPR008015. PDED_dom.
IPR017287. Rhodop-sen_GMP-Pdiesterase_dsu.
[Graphical view]
PfamiPF05351. GMP_PDE_delta. 1 hit.
[Graphical view]
PIRSFiPIRSF037825. GMP-Pdiesterase_delta. 1 hit.
SUPFAMiSSF81296. SSF81296. 1 hit.

Sequencei

Sequence statusi: Complete.

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

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.

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[»]
ProteinModelPortaliO43924.
SMRiO43924.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111173. 26 interactors.
DIPiDIP-36660N.
IntActiO43924. 17 interactors.
MINTiMINT-236371.
STRINGi9606.ENSP00000287600.

Chemistry databases

BindingDBiO43924.
ChEMBLiCHEMBL3860.

Polymorphism and mutation databases

BioMutaiPDE6D.

Proteomic databases

EPDiO43924.
PaxDbiO43924.
PeptideAtlasiO43924.
PRIDEiO43924.

Protocols and materials databases

DNASUi5147.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000287600; ENSP00000287600; ENSG00000156973.
GeneIDi5147.
KEGGihsa:5147.

Organism-specific databases

CTDi5147.
DisGeNETi5147.
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.
OMAiSTNTWQN.
OrthoDBiEOG091G0SV1.
PhylomeDBiO43924.
TreeFamiTF314474.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000156973-MONOMER.
ReactomeiR-HSA-5624958. ARL13B-mediated ciliary trafficking of INPP5E.

Miscellaneous databases

ChiTaRSiPDE6D. human.
EvolutionaryTraceiO43924.
GeneWikiiPDE6D.
GenomeRNAii5147.
PROiO43924.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000156973.
CleanExiHS_PDE6D.
ExpressionAtlasiO43924. baseline and differential.
GenevisibleiO43924. HS.

Family and domain databases

Gene3Di2.70.50.40. 1 hit.
InterProiIPR014756. Ig_E-set.
IPR008015. PDED_dom.
IPR017287. Rhodop-sen_GMP-Pdiesterase_dsu.
[Graphical view]
PfamiPF05351. GMP_PDE_delta. 1 hit.
[Graphical view]
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 historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: June 1, 1998
Last modified: November 30, 2016
This is version 151 of the entry and version 1 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 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.