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==The crystal structure of the RPGR RCC1-like domain in complex with PDE6D==
==The crystal structure of the RPGR RCC1-like domain in complex with PDE6D==
<StructureSection load='4jhp' size='340' side='right' caption='[[4jhp]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='4jhp' size='340' side='right'caption='[[4jhp]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4jhp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JHP FirstGlance]. <br>
<table><tr><td colspan='2'>[[4jhp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JHP FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jhn|4jhn]]</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDE6D, PDED ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RPGR, RP3, XLRP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4jhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhp OCA], [https://pdbe.org/4jhp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jhp RCSB], [https://www.ebi.ac.uk/pdbsum/4jhp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhp ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4jhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jhp RCSB], [http://www.ebi.ac.uk/pdbsum/4jhp PDBsum]</span></td></tr>
</table>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/RPGR_HUMAN RPGR_HUMAN]] Primary ciliary dyskinesia;Achromatopsia;Primary ciliary dyskinesia - retinitis pigmentosa;Cone rod dystrophy;Retinitis pigmentosa. Defects in RPGR are the cause of retinitis pigmentosa type 3 (RP3) [MIM:[http://omim.org/entry/300029 300029]]; also known as X-linked retinitis pigmentosa 3 (XLRP-3) or retinitis pigmentosa type 15 (RP15). A X-linked retinal dystrophy belonging to the group of pigmentary retinopathies. RP 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. In RP3, affected males have a severe phenotype, and carrier females show a wide spectrum of clinical features ranging from completely asymptomatic to severe retinitis pigmentosa. Heterozygous women can manifest a form of choroidoretinal degeneration which is distinguished from other types by the absence of visual defects in the presence of a brilliant, scintillating, golden-hued, patchy appearance most striking around the macula, called a tapetal-like retinal reflex.<ref>PMID:9990021</ref> <ref>PMID:8673101</ref> <ref>PMID:8817343</ref> <ref>PMID:10932196</ref> <ref>PMID:10970770</ref> <ref>PMID:9399904</ref> <ref>PMID:9855162</ref> <ref>PMID:10482958</ref> <ref>PMID:10737996</ref> <ref>PMID:10937588</ref> <ref>PMID:11180598</ref> <ref>PMID:11992260</ref> <ref>PMID:14564670</ref> <ref>PMID:12657579</ref>  Defects in RPGR are the cause of retinitis pigmentosa and sinorespiratory infections with or without deafness (RPDSI) [MIM:[http://omim.org/entry/300455 300455]]. A disease characterized by the association primary ciliary dyskinesia features with retinitis pigmentosa. Some patients also manifest deafness.<ref>PMID:12920075</ref> <ref>PMID:14627685</ref>  Defects in RPGR are the cause of cone-rod dystrophy X-linked type 1 (CORDX1) [MIM:[http://omim.org/entry/304020 304020]]; also known as cone dystrophy 1 (CO1). CORDs are inherited retinal dystrophies belonging to the group of pigmentary retinopathies. CORDs are characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa. In CORDX1 the degree of rod-photoreceptor involvement can be variable, with degeneration increasing as the disease progresses. Affected individuals (essentially all of whom are males) present with decreased visual acuity, myopia, photophobia, abnormal color vision, full peripheral visual fields, decreased photopic electroretinographic responses, and granularity of the macular retinal pigment epithelium. Although penetrance appears to be nearly 100%, there is variable expressivity with respect to age at onset and severity of symptoms.<ref>PMID:11857109</ref>  Defects in RPGR are a cause of macular degeneration X-linked atrophic (MDXLA) [MIM:[http://omim.org/entry/300834 300834]]. MDXLA is an ocular disorder characterized by macular atrophy causing progressive loss of visual acuity with minimal peripheral visual impairment. Some patients manifest extensive macular degeneration plus peripheral loss of retinal pigment epithelium and choriocapillaries. Full-field electroretinograms (ERGs) show normal cone and rod responses in some affected males despite advanced macular degeneration.<ref>PMID:12160730</ref> 
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/PDE6D_HUMAN PDE6D_HUMAN]] 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). [[http://www.uniprot.org/uniprot/RPGR_HUMAN RPGR_HUMAN]] Could be a guanine-nucleotide releasing factor. Plays a role in ciliogenesis. Probably regulates cilia formation by regulating actin stress filaments and cell contractility. Plays an important role in photoreceptor integrity. May play a critical role in spermatogenesis and in intraflagellar transport processes (By similarity). May be involved in microtubule organization and regulation of transport in primary cilia.<ref>PMID:21933838</ref> 
[https://www.uniprot.org/uniprot/PDE6D_HUMAN PDE6D_HUMAN] 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).
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 4jhp" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Phosphodiesterase|Phosphodiesterase]]
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Ismail, S]]
[[Category: Large Structures]]
[[Category: Vetter, I]]
[[Category: Ismail S]]
[[Category: Waetzlich, D]]
[[Category: Vetter I]]
[[Category: Wittinghofer, A]]
[[Category: Waetzlich D]]
[[Category: Beta propellar]]
[[Category: Wittinghofer A]]
[[Category: Immunoglobulin-like beta-sandwich]]
[[Category: Lipid binding protein]]
[[Category: Rcc1-like domain]]
[[Category: Seven bladed-propeller]]
[[Category: Structural protein]]

Latest revision as of 18:42, 20 September 2023

The crystal structure of the RPGR RCC1-like domain in complex with PDE6DThe crystal structure of the RPGR RCC1-like domain in complex with PDE6D

Structural highlights

4jhp is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDE6D_HUMAN 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).

Publication Abstract from PubMed

Defects in primary cilia result in human diseases known as ciliopathies. The retinitis pigmentosa GTPase regulator (RPGR), mutated in the most severe form of the eye disease, is located at the transition zone of the ciliary organelle. The RPGR-interacting partner PDEdelta is involved in trafficking of farnesylated ciliary cargo, but the significance of this interaction is unknown. The crystal structure of the propeller domain of RPGR shows the location of patient mutations and how they perturb the structure. The RPGR.PDEdelta complex structure shows PDEdelta on a highly conserved surface patch of RPGR. Biochemical experiments and structural considerations show that RPGR can bind with high affinity to cargo-loaded PDEdelta and exposes the Arl2/Arl3-binding site on PDEdelta. On the basis of these results, we propose a model where RPGR is acting as a scaffold protein recruiting cargo-loaded PDEdelta and Arl3 to release lipidated cargo into cilia.

The interplay between RPGR, PDEdelta and Arl2/3 regulate the ciliary targeting of farnesylated cargo.,Watzlich D, Vetter I, Gotthardt K, Miertzschke M, Chen YX, Wittinghofer A, Ismail S EMBO Rep. 2013 Apr 5. doi: 10.1038/embor.2013.37. PMID:23559067[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Watzlich D, Vetter I, Gotthardt K, Miertzschke M, Chen YX, Wittinghofer A, Ismail S. The interplay between RPGR, PDEdelta and Arl2/3 regulate the ciliary targeting of farnesylated cargo. EMBO Rep. 2013 Apr 5. doi: 10.1038/embor.2013.37. PMID:23559067 doi:10.1038/embor.2013.37

4jhp, resolution 1.90Å

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