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

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O43924 (PDE6D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 114. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Short name=GMP-PDE delta

Alternative name(s):
Protein p17

Gene names

Name:	PDE6D
Synonyms:	PDED

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	150 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as a GTP specific dissociation inhibitor (GDI). Increases the affinity of ARL3 for GTP by several orders of magnitude and does so by decreasing the nucleotide dissociation rate. Stabilizes Arl3-GTP by decreasing the nucleotide dissociation By similarity.
Subunit structure	Interacts with ARL2, ARL3, and RPGR. Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain. Interacts with ARL3; the interaction occurs specifically with the GTP-bound form of ARL3 By similarity. Interacts with HRAS and RPGR. Ref.7 Ref.8 Ref.10
Tissue specificity	Retina.
Sequence similarities	Belongs to the PDE6D/unc-119 family.

Ontologies

Keywords
Biological process	Sensory transduction Vision
Ligand	cGMP
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	regulation of GTP catabolic process Inferred from sequence or structural similarity. Source: UniProtKB response to stimulus Inferred from electronic annotation. Source: UniProtKB-KW visual perception Traceable author statement Ref.1. Source: ProtInc
Molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity Inferred from electronic annotation. Source: InterPro GTPase inhibitor activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Arl2	Q9D0J4	3	EBI-712685,EBI-1033319	From a different organism.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 150

150

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

PRO_0000221208

Experimental info

Sequence conflict

117

M → V in CAA04880. Ref.4

Sequence conflict

146

R → G in CAA04880. Ref.4

Secondary structure

150

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

O43924 [UniParc].

Last modified June 1, 1998. Version 1.
Checksum: AB8D9309C33B4411
Show »

FASTA

150

17,420

        10         20         30         40         50         60 
MSAKDERARE ILRGFKLNWM NLRDAETGKI LWQGTEDLSV PGVEHEARVP KKILKCKAVS 

        70         80         90        100        110        120 
RELNFSSTEQ MEKFRLEQKV YFKGQCLEEW FFEFGFVIPN STNTWQSLIE AAPESQMMPA 

       130        140        150 
SVLTGNVIIE TKFFDDDLLV STSRVRLFYV

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of human and mouse rod cGMP phosphodiesterase delta subunit (PDE6D) and chromosomal localization of the human gene." Li N., Florio S.K., Pettenati M.J., Rao P.N., Beavo J.A., Baehr W. Genomics 49:76-82(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"cDNA sequence, genomic organization and mapping of PDE6D, the human gene encoding the delta subunit of the cGMP phosphodiesterase of retinal rod cells to chromosome 2q36." Erchova G., Derre J., Chatelin S., Nancy V., Berger R., Kaplan J., Munnich A., de Gunzburg J. Cytogenet. Cell Genet. 79:139-141(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"Cloning and gene structure of the rod cGMP phosphodiesterase delta subunit gene (PDED) in man and mouse." Lorenz B., Migliaccio C., Lichtner P., Meyer C., Strom T.M., D'Urso M., Becker J., Ciccodicola A., Meitinger T. Eur. J. Hum. Genet. 6:283-290(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"A novel RAB interacting protein." Zahraoui A., Marzesco A.-M., Galli T., Louvard D. Submitted (SEP-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[5]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Placenta.
[7]	"The delta subunit of rod specific cyclic GMP phosphodiesterase, PDE delta, interacts with the Arf-like protein Arl3 in a GTP specific manner." Linari M., Hanzal-Bayer M., Becker J. FEBS Lett. 458:55-59(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ARL3.
[8]	"The retinitis pigmentosa GTPase regulator, RPGR, interacts with the delta subunit of rod cyclic GMP phosphodiesterase." Linari M., Ueffing M., Manson F., Wright A., Meitinger T., Becker J. Proc. Natl. Acad. Sci. U.S.A. 96:1315-1320(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RPGR.
[9]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]	"The complex of Arl2-GTP and PDE delta: from structure to function." Hanzal-Bayer M., Renault L., Roversi P., Wittinghofer A., Hillig R.C. EMBO J. 21:2095-2106(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH MOUSE ARL2 AND GTP, INTERACTION WITH HRAS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00015161.

RefSeq

NP_002592.1. NM_002601.2.

UniGene

Hs.516808.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KSG	X-ray	2.30	B	1-150	[»]
1KSH	X-ray	1.80	B	1-150	[»]
1KSJ	X-ray	2.60	B	1-150	[»]
3T5G	X-ray	1.70	B	1-150	[»]
3T5I	X-ray	2.10	A/B/C/D	1-150	[»]

ProteinModelPortal

O43924.

ModBase

Search...

Protein-protein interaction databases

IntAct

O43924. 9 interactions.

MINT

MINT-236371.

STRING

9606.ENSP00000287600.

Proteomic databases

PaxDb

O43924.

PRIDE

O43924.

Protocols and materials databases

DNASU

5147.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000287600; ENSP00000287600; ENSG00000156973.

GeneID

5147.

KEGG

hsa:5147.

UCSC

uc002vse.1. human.

Organism-specific databases

CTD

5147.

GeneCards

GC02M232597.

HGNC

HGNC:8788. PDE6D.

HPA

HPA037434.

MIM

602676. gene.

neXtProt

NX_O43924.

PharmGKB

PA33136.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG302334.

HOGENOM

HOG000007689.

HOVERGEN

HBG053542.

InParanoid

O43924.

K13758.

OMA

FVIPDST.

OrthoDB

EOG4G1MHN.

PhylomeDB

O43924.

Gene expression databases

ArrayExpress

O43924.

Bgee

O43924.

CleanEx

HS_PDE6D.

Genevestigator

O43924.

GermOnline

ENSG00000156973. Homo sapiens.

Family and domain databases

Gene3D

2.70.50.40. 1 hit.

InterPro

IPR008015. GMP_PDE_delta.
IPR014756. Ig_E-set.
IPR017287. Rhodop-sen_GMP-Pdiesterase_dsu.
[Graphical view]

Pfam

PF05351. GMP_PDE_delta. 1 hit.
[Graphical view]

PIRSF

PIRSF037825. GMP-Pdiesterase_delta. 1 hit.

SUPFAM

SSF81296. Ig_E-set. 1 hit.

ProtoNet

Search...

Other

BindingDB

O43924.

ChEMBL

CHEMBL3860.

ChiTaRS

PDE6D. human.

EvolutionaryTrace

O43924.

GenomeRNAi

5147.

NextBio

19860.

SOURCE

Search...

Entry information

Entry name

PDE6D_HUMAN

Accession

Primary (citable) accession number: O43924
Secondary accession number(s): O43250

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1999
Last sequence update:	June 1, 1998
Last modified:	May 1, 2013
This is version 114 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.

Relevant documents

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents