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Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (GMP-PDE delta) (Protein p17)

 PDE6D_HUMAN             Reviewed;         150 AA.
O43924; O43250;
15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
01-JUN-1998, sequence version 1.
05-JUL-2017, entry version 157.
RecName: Full=Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta;
Short=GMP-PDE delta;
AltName: Full=Protein p17;
Name=PDE6D; Synonyms=PDED;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=9570951; DOI=10.1006/geno.1998.5210;
Li N., Florio S.K., Pettenati M.J., Rao P.N., Beavo J.A., Baehr W.;
"Characterization of human and mouse rod cGMP phosphodiesterase delta
subunit (PDE6D) and chromosomal localization of the human gene.";
Genomics 49:76-82(1998).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=9533031;
Erchova G., Derre J., Chatelin S., Nancy V., Berger R., Kaplan J.,
Munnich A., de Gunzburg J.;
"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.";
Cytogenet. Cell Genet. 79:139-141(1997).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=9781033; DOI=10.1038/sj.ejhg.5200215;
Lorenz B., Migliaccio C., Lichtner P., Meyer C., Strom T.M.,
D'Urso M., Becker J., Ciccodicola A., Meitinger T.;
"Cloning and gene structure of the rod cGMP phosphodiesterase delta
subunit gene (PDED) in man and mouse.";
Eur. J. Hum. Genet. 6:283-290(1998).
[4]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH RAB13,
SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
PubMed=9712853; DOI=10.1074/jbc.273.35.22340;
Marzesco A.M., Galli T., Louvard D., Zahraoui A.;
"The rod cGMP phosphodiesterase delta subunit dissociates the small
GTPase Rab13 from membranes.";
J. Biol. Chem. 273:22340-22345(1998).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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.;
"Cloning of human full-length CDSs in BD Creator(TM) system donor
vector.";
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Placenta;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[7]
INTERACTION WITH ARL3.
PubMed=10518933; DOI=10.1016/S0014-5793(99)01117-5;
Linari M., Hanzal-Bayer M., Becker J.;
"The delta subunit of rod specific cyclic GMP phosphodiesterase, PDE
delta, interacts with the Arf-like protein Arl3 in a GTP specific
manner.";
FEBS Lett. 458:55-59(1999).
[8]
INTERACTION WITH RPGR.
PubMed=9990021; DOI=10.1073/pnas.96.4.1315;
Linari M., Ueffing M., Manson F., Wright A., Meitinger T., Becker J.;
"The retinitis pigmentosa GTPase regulator, RPGR, interacts with the
delta subunit of rod cyclic GMP phosphodiesterase.";
Proc. Natl. Acad. Sci. U.S.A. 96:1315-1320(1999).
[9]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[10]
INVOLVEMENT IN JBTS22, FUNCTION, INTERACTION WITH RPGR; ARL2; ARL3 AND
INPP5E, AND SUBCELLULAR LOCATION.
PubMed=24166846; DOI=10.1002/humu.22470;
Thomas S., Wright K.J., Le Corre S., Micalizzi A., Romani M.,
Abhyankar A., Saada J., Perrault I., Amiel J., Litzler J., Filhol E.,
Elkhartoufi N., Kwong M., Casanova J.L., Boddaert N., Baehr W.,
Lyonnet S., Munnich A., Burglen L., Chassaing N., Encha-Ravazi F.,
Vekemans M., Gleeson J.G., Valente E.M., Jackson P.K., Drummond I.A.,
Saunier S., Attie-Bitach T.;
"A homozygous PDE6D mutation in Joubert syndrome impairs targeting of
farnesylated INPP5E protein to the primary cilium.";
Hum. Mutat. 35:137-146(2014).
[11]
X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH MOUSE ARL2 AND
GTP, AND INTERACTION WITH HRAS.
PubMed=11980706; DOI=10.1093/emboj/21.9.2095;
Hanzal-Bayer M., Renault L., Roversi P., Wittinghofer A., Hillig R.C.;
"The complex of Arl2-GTP and PDE delta: from structure to function.";
EMBO J. 21:2095-2106(2002).
[12]
X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH RHEB, FUNCTION,
INTERACTION WITH RHEB; NRAS AND ARL2, AND SUBCELLULAR LOCATION.
PubMed=22002721; DOI=10.1038/nchembio.686;
Ismail S.A., Chen Y.X., Rusinova A., Chandra A., Bierbaum M.,
Gremer L., Triola G., Waldmann H., Bastiaens P.I., Wittinghofer A.;
"Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for
farnesylated cargo.";
Nat. Chem. Biol. 7:942-949(2011).
[13]
X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH RPGR, FUNCTION,
AND INTERACTION WITH RPGR.
PubMed=23559067; DOI=10.1038/embor.2013.37;
Watzlich D., Vetter I., Gotthardt K., Miertzschke M., Chen Y.X.,
Wittinghofer A., Ismail S.;
"The interplay between RPGR, PDE? and Arl2/3 regulate the ciliary
targeting of farnesylated cargo.";
EMBO Rep. 14:465-472(2013).
[14]
X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS), FUNCTION, INTERACTION WITH
RHEB AND KRAS, AND SUBCELLULAR LOCATION.
PubMed=23698361; DOI=10.1038/nature12205;
Zimmermann G., Papke B., Ismail S., Vartak N., Chandra A.,
Hoffmann M., Hahn S.A., Triola G., Wittinghofer A., Bastiaens P.I.,
Waldmann H.;
"Small molecule inhibition of the KRAS-PDE? interaction impairs
oncogenic KRAS signalling.";
Nature 497:638-642(2013).
-!- FUNCTION: 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).
{ECO:0000250|UniProtKB:O55057, ECO:0000269|PubMed:10518933,
ECO:0000269|PubMed:22002721, ECO:0000269|PubMed:23559067,
ECO:0000269|PubMed:23698361, ECO:0000269|PubMed:24166846,
ECO:0000269|PubMed:9712853}.
-!- SUBUNIT: 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).
{ECO:0000250|UniProtKB:O55057, ECO:0000250|UniProtKB:Q95142,
ECO:0000269|PubMed:10518933, ECO:0000269|PubMed:11980706,
ECO:0000269|PubMed:22002721, ECO:0000269|PubMed:23559067,
ECO:0000269|PubMed:23698361, ECO:0000269|PubMed:24166846,
ECO:0000269|PubMed:9990021}.
-!- INTERACTION:
Q0P5N6:ARL16; NbExp=9; IntAct=EBI-712685, EBI-10186132;
P36404:ARL2; NbExp=16; IntAct=EBI-712685, EBI-752365;
Q9D0J4:Arl2 (xeno); NbExp=6; IntAct=EBI-712685, EBI-1033319;
P36405:ARL3; NbExp=4; IntAct=EBI-712685, EBI-712710;
Q9WUL7:Arl3 (xeno); NbExp=4; IntAct=EBI-712685, EBI-6860857;
P51153:RAB13; NbExp=2; IntAct=EBI-712685, EBI-1780121;
Q15382:RHEB; NbExp=5; IntAct=EBI-712685, EBI-6860739;
Q92834:RPGR; NbExp=9; IntAct=EBI-712685, EBI-6558417;
Q7DB77:tir (xeno); NbExp=3; IntAct=EBI-712685, EBI-6480811;
-!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
{ECO:0000269|PubMed:22002721, ECO:0000269|PubMed:23698361,
ECO:0000269|PubMed:9712853}. Cytoplasmic vesicle membrane
{ECO:0000269|PubMed:9712853}; Peripheral membrane protein
{ECO:0000269|PubMed:9712853}. Cytoplasm, cytoskeleton, cilium
basal body {ECO:0000269|PubMed:24166846}.
-!- TISSUE SPECIFICITY: Widely expressed. Detected in various tissues
including spleen, prostate gland, testis, ovary, small intestine,
colon, retina, and peripheral blood. {ECO:0000269|PubMed:9712853}.
-!- DISEASE: Joubert syndrome 22 (JBTS22) [MIM:615665]: A 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.
{ECO:0000269|PubMed:24166846}. Note=The disease is caused by
mutations affecting the gene represented in this entry.
-!- SIMILARITY: Belongs to the PDE6D/unc-119 family. {ECO:0000305}.
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EMBL; AF045999; AAC39720.1; -; Genomic_DNA.
EMBL; AF022912; AAB87872.1; -; mRNA.
EMBL; AF042835; AAC25953.1; -; Genomic_DNA.
EMBL; AF042833; AAC25953.1; JOINED; Genomic_DNA.
EMBL; AF042834; AAC25953.1; JOINED; Genomic_DNA.
EMBL; AJ001626; CAA04880.1; -; mRNA.
EMBL; BT007278; AAP35942.1; -; mRNA.
EMBL; BC007831; AAH07831.1; -; mRNA.
CCDS; CCDS33398.1; -.
RefSeq; NP_001277947.1; NM_001291018.1.
RefSeq; NP_002592.1; NM_002601.3.
UniGene; Hs.516808; -.
PDB; 1KSG; X-ray; 2.30 A; B=1-150.
PDB; 1KSH; X-ray; 1.80 A; B=1-150.
PDB; 1KSJ; X-ray; 2.60 A; B=1-150.
PDB; 3T5G; X-ray; 1.70 A; B=1-150.
PDB; 3T5I; X-ray; 2.10 A; A/B/C/D=1-150.
PDB; 4JHP; X-ray; 1.90 A; B=1-150.
PDB; 4JV6; X-ray; 1.87 A; B=1-150.
PDB; 4JV8; X-ray; 1.45 A; B=1-150.
PDB; 4JVB; X-ray; 1.75 A; B=1-150.
PDB; 4JVF; X-ray; 2.40 A; B=1-150.
PDB; 5E80; X-ray; 2.60 A; A/B=2-150.
PDB; 5E8F; X-ray; 2.10 A; A/C=2-150.
PDB; 5F2U; X-ray; 1.85 A; A/B=2-150.
PDB; 5ML2; X-ray; 1.60 A; B=2-150.
PDB; 5ML3; X-ray; 1.40 A; B=2-150.
PDB; 5ML4; X-ray; 2.40 A; B=2-150.
PDB; 5ML6; X-ray; 1.87 A; B=2-150.
PDB; 5ML8; X-ray; 2.60 A; B=2-150.
PDB; 5NAL; X-ray; 2.20 A; B=1-150.
PDB; 5TAR; X-ray; 1.90 A; B=3-150.
PDB; 5TB5; X-ray; 2.00 A; B/D=1-150.
PDBsum; 1KSG; -.
PDBsum; 1KSH; -.
PDBsum; 1KSJ; -.
PDBsum; 3T5G; -.
PDBsum; 3T5I; -.
PDBsum; 4JHP; -.
PDBsum; 4JV6; -.
PDBsum; 4JV8; -.
PDBsum; 4JVB; -.
PDBsum; 4JVF; -.
PDBsum; 5E80; -.
PDBsum; 5E8F; -.
PDBsum; 5F2U; -.
PDBsum; 5ML2; -.
PDBsum; 5ML3; -.
PDBsum; 5ML4; -.
PDBsum; 5ML6; -.
PDBsum; 5ML8; -.
PDBsum; 5NAL; -.
PDBsum; 5TAR; -.
PDBsum; 5TB5; -.
ProteinModelPortal; O43924; -.
SMR; O43924; -.
BioGrid; 111173; 26.
DIP; DIP-36660N; -.
IntAct; O43924; 18.
MINT; MINT-236371; -.
STRING; 9606.ENSP00000287600; -.
BindingDB; O43924; -.
ChEMBL; CHEMBL3860; -.
BioMuta; PDE6D; -.
EPD; O43924; -.
PaxDb; O43924; -.
PeptideAtlas; O43924; -.
PRIDE; O43924; -.
DNASU; 5147; -.
Ensembl; ENST00000287600; ENSP00000287600; ENSG00000156973.
GeneID; 5147; -.
KEGG; hsa:5147; -.
CTD; 5147; -.
DisGeNET; 5147; -.
GeneCards; PDE6D; -.
HGNC; HGNC:8788; PDE6D.
HPA; HPA037433; -.
HPA; HPA037434; -.
MalaCards; PDE6D; -.
MIM; 602676; gene.
MIM; 615665; phenotype.
neXtProt; NX_O43924; -.
OpenTargets; ENSG00000156973; -.
Orphanet; 2754; Joubert syndrome with orofaciodigital defect.
PharmGKB; PA33136; -.
eggNOG; KOG4038; Eukaryota.
eggNOG; ENOG4110ZMQ; LUCA.
GeneTree; ENSGT00390000000263; -.
HOGENOM; HOG000007689; -.
HOVERGEN; HBG053542; -.
KO; K13758; -.
OMA; LWQGNED; -.
OrthoDB; EOG091G0SV1; -.
PhylomeDB; O43924; -.
TreeFam; TF314474; -.
Reactome; R-HSA-5624958; ARL13B-mediated ciliary trafficking of INPP5E.
ChiTaRS; PDE6D; human.
EvolutionaryTrace; O43924; -.
GeneWiki; PDE6D; -.
GenomeRNAi; 5147; -.
PRO; PR:O43924; -.
Proteomes; UP000005640; Chromosome 2.
Bgee; ENSG00000156973; -.
CleanEx; HS_PDE6D; -.
ExpressionAtlas; O43924; baseline and differential.
Genevisible; O43924; HS.
GO; GO:0005929; C:cilium; TAS:Reactome.
GO; GO:0031410; C:cytoplasmic vesicle; IDA:UniProtKB.
GO; GO:0030659; C:cytoplasmic vesicle membrane; IEA:UniProtKB-SubCell.
GO; GO:0005856; C:cytoskeleton; IEA:UniProtKB-KW.
GO; GO:0005829; C:cytosol; IDA:UniProtKB.
GO; GO:0004114; F:3',5'-cyclic-nucleotide phosphodiesterase activity; IEA:InterPro.
GO; GO:0005095; F:GTPase inhibitor activity; ISS:UniProtKB.
GO; GO:0017137; F:Rab GTPase binding; IPI:UniProtKB.
GO; GO:0050896; P:response to stimulus; IEA:UniProtKB-KW.
GO; GO:0007601; P:visual perception; TAS:ProtInc.
Gene3D; 2.70.50.40; -; 1.
InterPro; IPR014756; Ig_E-set.
InterPro; IPR008015; PDED_dom.
InterPro; IPR017287; Rhodop-sen_GMP-Pdiesterase_dsu.
Pfam; PF05351; GMP_PDE_delta; 1.
PIRSF; PIRSF037825; GMP-Pdiesterase_delta; 1.
SUPFAM; SSF81296; SSF81296; 1.
1: Evidence at protein level;
3D-structure; Cell projection; cGMP; Ciliopathy; Complete proteome;
Cytoplasm; Cytoplasmic vesicle; Cytoskeleton; Joubert syndrome;
Membrane; Reference proteome; Sensory transduction; Vision.
CHAIN 1 150 Retinal rod rhodopsin-sensitive cGMP
3',5'-cyclic phosphodiesterase subunit
delta.
/FTId=PRO_0000221208.
REGION 144 150 Required for association with membranes.
{ECO:0000269|PubMed:9712853}.
CONFLICT 117 117 M -> V (in Ref. 4; CAA04880).
{ECO:0000305}.
CONFLICT 146 146 R -> G (in Ref. 4; CAA04880).
{ECO:0000305}.
HELIX 3 13 {ECO:0000244|PDB:5ML3}.
STRAND 15 24 {ECO:0000244|PDB:5ML3}.
TURN 25 27 {ECO:0000244|PDB:5ML3}.
STRAND 30 34 {ECO:0000244|PDB:5ML3}.
STRAND 43 50 {ECO:0000244|PDB:5ML3}.
HELIX 51 55 {ECO:0000244|PDB:5ML3}.
STRAND 57 69 {ECO:0000244|PDB:5ML3}.
STRAND 71 82 {ECO:0000244|PDB:5ML3}.
STRAND 85 97 {ECO:0000244|PDB:5ML3}.
STRAND 101 110 {ECO:0000244|PDB:5ML3}.
HELIX 114 116 {ECO:0000244|PDB:3T5G}.
HELIX 120 123 {ECO:0000244|PDB:5ML3}.
TURN 124 126 {ECO:0000244|PDB:5ML3}.
STRAND 127 135 {ECO:0000244|PDB:5ML3}.
STRAND 138 150 {ECO:0000244|PDB:5ML3}.
SEQUENCE 150 AA; 17420 MW; AB8D9309C33B4411 CRC64;
MSAKDERARE ILRGFKLNWM NLRDAETGKI LWQGTEDLSV PGVEHEARVP KKILKCKAVS
RELNFSSTEQ MEKFRLEQKV YFKGQCLEEW FFEFGFVIPN STNTWQSLIE AAPESQMMPA
SVLTGNVIIE TKFFDDDLLV STSRVRLFYV


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547, Yurok Circle
San Jose, CA 95123
CA 95123
Tel (408) 780-0908,
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Genprice Inc, Invoices and accounting
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San Jose, CA 95123




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NL850396268B01 KVK nummer 52327027
Kuiper 1
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