3bh6

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the RP2-Arl3 complex bound to GppNHp

Structural highlights

3bh6 is a 2 chain structure with sequence from Homo sapiens and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

XRP2_HUMAN Defects in RP2 are the cause of retinitis pigmentosa type 2 (RP2) [MIM:312600; also known as X-linked retinitis pigmentosa 2 (XLRP-2). RP leads to degeneration of retinal photoreceptor cells. 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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Function

XRP2_HUMAN Acts as a GTPase-activating protein (GAP) involved in trafficking between the Golgi and the ciliary membrane. Involved in localization of proteins, such as NPHP3, to the cilium membrane by inducing hydrolysis of GTP ARL3, leading to the release of UNC119 (or UNC119B). Acts as a GTPase-activating protein (GAP) for tubulin in concert with tubulin-specific chaperone C, but does not enhance tubulin heterodimerization. Acts as guanine nucleotide dissociation inhibitor towards ADP-ribosylation factor-like proteins.^[14] ^[15] ^[16] ^[17]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The retinitis pigmentosa 2 (RP2) gene is responsible for a particular variant of X chromosome-linked eye disease. Previously, RP2 was shown to bind the GTP form of the small G protein Arf-like 3 (Arl3), thus qualifying as an effector. Here we present the Arl3-GppNHp-RP2 complex structure, which shows features resembling complexes with GTPase-activating proteins (GAPs). Biochemical analysis showing a 90,000-fold stimulation of the GTPase reaction together with the structure of an Arl3-GDP-AlF4--RP2 transition state complex showed that RP2 is an efficient GAP for Arl3, with structural features similar to other GAPs. Furthermore, the effect of mutations in patients with retinitis pigmentosa correlated with their effect on catalysis, in particular the mutation of the arginine finger of RP2. The cognate G protein-GAP pair is conserved in yeast as Cin4-Cin2, and the ability of RP2 to act as a GAP can be correlated with its ability to complement a CIN2-deletion phenotype.

The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3.,Veltel S, Gasper R, Eisenacher E, Wittinghofer A Nat Struct Mol Biol. 2008 Apr;15(4):373-80. Epub 2008 Mar 23. PMID:18376416^[18]

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

References

↑ Bartolini F, Bhamidipati A, Thomas S, Schwahn U, Lewis SA, Cowan NJ. Functional overlap between retinitis pigmentosa 2 protein and the tubulin-specific chaperone cofactor C. J Biol Chem. 2002 Apr 26;277(17):14629-34. Epub 2002 Feb 14. PMID:11847227 doi:10.1074/jbc.M200128200
↑ Kuhnel K, Veltel S, Schlichting I, Wittinghofer A. Crystal structure of the human retinitis pigmentosa 2 protein and its interaction with Arl3. Structure. 2006 Feb;14(2):367-78. PMID:16472755 doi:10.1016/j.str.2005.11.008
↑ Chapple JP, Hardcastle AJ, Grayson C, Spackman LA, Willison KR, Cheetham ME. Mutations in the N-terminus of the X-linked retinitis pigmentosa protein RP2 interfere with the normal targeting of the protein to the plasma membrane. Hum Mol Genet. 2000 Aug 12;9(13):1919-26. PMID:10942419
↑ Schwahn U, Lenzner S, Dong J, Feil S, Hinzmann B, van Duijnhoven G, Kirschner R, Hemberger M, Bergen AA, Rosenberg T, Pinckers AJ, Fundele R, Rosenthal A, Cremers FP, Ropers HH, Berger W. Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nat Genet. 1998 Aug;19(4):327-32. PMID:9697692 doi:10.1038/1214
↑ Hardcastle AJ, Thiselton DL, Van Maldergem L, Saha BK, Jay M, Plant C, Taylor R, Bird AC, Bhattacharya S. Mutations in the RP2 gene cause disease in 10% of families with familial X-linked retinitis pigmentosa assessed in this study. Am J Hum Genet. 1999 Apr;64(4):1210-5. PMID:10090907
↑ Rosenberg T, Schwahn U, Feil S, Berger W. Genotype-phenotype correlation in X-linked retinitis pigmentosa 2 (RP2). Ophthalmic Genet. 1999 Sep;20(3):161-72. PMID:10520237
↑ Wada Y, Nakazawa M, Abe T, Tamai M. A new Leu253Arg mutation in the RP2 gene in a Japanese family with X-linked retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2000 Jan;41(1):290-3. PMID:10634633
↑ Sharon D, Bruns GA, McGee TL, Sandberg MA, Berson EL, Dryja TP. X-linked retinitis pigmentosa: mutation spectrum of the RPGR and RP2 genes and correlation with visual function. Invest Ophthalmol Vis Sci. 2000 Aug;41(9):2712-21. PMID:10937588
↑ Miano MG, Testa F, Filippini F, Trujillo M, Conte I, Lanzara C, Millan JM, De Bernardo C, Grammatico B, Mangino M, Torrente I, Carrozzo R, Simonelli F, Rinaldi E, Ventruto V, D'Urso M, Ayuso C, Ciccodicola A. Identification of novel RP2 mutations in a subset of X-linked retinitis pigmentosa families and prediction of new domains. Hum Mutat. 2001 Aug;18(2):109-19. PMID:11462235 doi:10.1002/humu.1160
↑ Breuer DK, Yashar BM, Filippova E, Hiriyanna S, Lyons RH, Mears AJ, Asaye B, Acar C, Vervoort R, Wright AF, Musarella MA, Wheeler P, MacDonald I, Iannaccone A, Birch D, Hoffman DR, Fishman GA, Heckenlively JR, Jacobson SG, Sieving PA, Swaroop A. A comprehensive mutation analysis of RP2 and RPGR in a North American cohort of families with X-linked retinitis pigmentosa. Am J Hum Genet. 2002 Jun;70(6):1545-54. Epub 2002 Apr 30. PMID:11992260 doi:10.1086/340848
↑ Sharon D, Sandberg MA, Rabe VW, Stillberger M, Dryja TP, Berson EL. RP2 and RPGR mutations and clinical correlations in patients with X-linked retinitis pigmentosa. Am J Hum Genet. 2003 Nov;73(5):1131-46. Epub 2003 Oct 16. PMID:14564670 doi:S0002-9297(07)61975-2
↑ Bader I, Brandau O, Achatz H, Apfelstedt-Sylla E, Hergersberg M, Lorenz B, Wissinger B, Wittwer B, Rudolph G, Meindl A, Meitinger T. X-linked retinitis pigmentosa: RPGR mutations in most families with definite X linkage and clustering of mutations in a short sequence stretch of exon ORF15. Invest Ophthalmol Vis Sci. 2003 Apr;44(4):1458-63. PMID:12657579
↑ Neveling K, Collin RW, Gilissen C, van Huet RA, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FP, Scheffer H. Next-generation genetic testing for retinitis pigmentosa. Hum Mutat. 2012 Jun;33(6):963-72. doi: 10.1002/humu.22045. Epub 2012 Mar 19. PMID:22334370 doi:10.1002/humu.22045
↑ Bartolini F, Bhamidipati A, Thomas S, Schwahn U, Lewis SA, Cowan NJ. Functional overlap between retinitis pigmentosa 2 protein and the tubulin-specific chaperone cofactor C. J Biol Chem. 2002 Apr 26;277(17):14629-34. Epub 2002 Feb 14. PMID:11847227 doi:10.1074/jbc.M200128200
↑ Evans RJ, Schwarz N, Nagel-Wolfrum K, Wolfrum U, Hardcastle AJ, Cheetham ME. The retinitis pigmentosa protein RP2 links pericentriolar vesicle transport between the Golgi and the primary cilium. Hum Mol Genet. 2010 Apr 1;19(7):1358-67. doi: 10.1093/hmg/ddq012. Epub 2010 Jan, 27. PMID:20106869 doi:10.1093/hmg/ddq012
↑ Wright KJ, Baye LM, Olivier-Mason A, Mukhopadhyay S, Sang L, Kwong M, Wang W, Pretorius PR, Sheffield VC, Sengupta P, Slusarski DC, Jackson PK. An ARL3-UNC119-RP2 GTPase cycle targets myristoylated NPHP3 to the primary cilium. Genes Dev. 2011 Nov 15;25(22):2347-60. doi: 10.1101/gad.173054.111. PMID:22085962 doi:10.1101/gad.173443.111
↑ Veltel S, Gasper R, Eisenacher E, Wittinghofer A. The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3. Nat Struct Mol Biol. 2008 Apr;15(4):373-80. Epub 2008 Mar 23. PMID:18376416 doi:nsmb.1396
↑ Veltel S, Gasper R, Eisenacher E, Wittinghofer A. The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3. Nat Struct Mol Biol. 2008 Apr;15(4):373-80. Epub 2008 Mar 23. PMID:18376416 doi:nsmb.1396

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3bh6"

@@ Line 3: / Line 3: @@
 <StructureSection load='3bh6' size='340' side='right'caption='[[3bh6]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bh6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human] and [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BH6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bh6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BH6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bx6|2bx6]], [[3bh7|3bh7]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Arl3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), RP2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3bh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bh6 OCA], [https://pdbe.org/3bh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bh6 RCSB], [https://www.ebi.ac.uk/pdbsum/3bh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bh6 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/XRP2_HUMAN XRP2_HUMAN]] Defects in RP2 are the cause of retinitis pigmentosa type 2 (RP2) [MIM:[https://omim.org/entry/312600 312600]]; also known as X-linked retinitis pigmentosa 2 (XLRP-2). RP leads to degeneration of retinal photoreceptor cells. 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.<ref>PMID:11847227</ref> <ref>PMID:16472755</ref> <ref>PMID:10942419</ref> <ref>PMID:9697692</ref> <ref>PMID:10090907</ref> <ref>PMID:10520237</ref> <ref>PMID:10634633</ref> <ref>PMID:10937588</ref> <ref>PMID:11462235</ref> <ref>PMID:11992260</ref> <ref>PMID:14564670</ref> <ref>PMID:12657579</ref> <ref>PMID:22334370</ref>
+[https://www.uniprot.org/uniprot/XRP2_HUMAN XRP2_HUMAN] Defects in RP2 are the cause of retinitis pigmentosa type 2 (RP2) [MIM:[https://omim.org/entry/312600 312600]; also known as X-linked retinitis pigmentosa 2 (XLRP-2). RP leads to degeneration of retinal photoreceptor cells. 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.<ref>PMID:11847227</ref> <ref>PMID:16472755</ref> <ref>PMID:10942419</ref> <ref>PMID:9697692</ref> <ref>PMID:10090907</ref> <ref>PMID:10520237</ref> <ref>PMID:10634633</ref> <ref>PMID:10937588</ref> <ref>PMID:11462235</ref> <ref>PMID:11992260</ref> <ref>PMID:14564670</ref> <ref>PMID:12657579</ref> <ref>PMID:22334370</ref>
 == Function ==
-[[https://www.uniprot.org/uniprot/ARL3_MOUSE ARL3_MOUSE]] Small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP). Required for normal cytokinesis and cilia signaling. Required for targeting proteins such as NPHP3 to the ciliary membrane by releasing myristoylated NPHP3 from UNC119B cargo adapter into the cilium (By similarity). Requires assistance from GTPase-activating proteins (GAPs) like RP2 and PDE6D, in order to cycle between inactive GDP-bound and active GTP-bound forms.<ref>PMID:15979089</ref> <ref>PMID:18376416</ref>  [[https://www.uniprot.org/uniprot/XRP2_HUMAN XRP2_HUMAN]] Acts as a GTPase-activating protein (GAP) involved in trafficking between the Golgi and the ciliary membrane. Involved in localization of proteins, such as NPHP3, to the cilium membrane by inducing hydrolysis of GTP ARL3, leading to the release of UNC119 (or UNC119B). Acts as a GTPase-activating protein (GAP) for tubulin in concert with tubulin-specific chaperone C, but does not enhance tubulin heterodimerization. Acts as guanine nucleotide dissociation inhibitor towards ADP-ribosylation factor-like proteins.<ref>PMID:11847227</ref> <ref>PMID:20106869</ref> <ref>PMID:22085962</ref> <ref>PMID:18376416</ref>
+[https://www.uniprot.org/uniprot/XRP2_HUMAN XRP2_HUMAN] Acts as a GTPase-activating protein (GAP) involved in trafficking between the Golgi and the ciliary membrane. Involved in localization of proteins, such as NPHP3, to the cilium membrane by inducing hydrolysis of GTP ARL3, leading to the release of UNC119 (or UNC119B). Acts as a GTPase-activating protein (GAP) for tubulin in concert with tubulin-specific chaperone C, but does not enhance tubulin heterodimerization. Acts as guanine nucleotide dissociation inhibitor towards ADP-ribosylation factor-like proteins.<ref>PMID:11847227</ref> <ref>PMID:20106869</ref> <ref>PMID:22085962</ref> <ref>PMID:18376416</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Gasper, R]]
+[[Category: Gasper R]]
-[[Category: Veltel, S]]
+[[Category: Veltel S]]
-[[Category: Wittinghofer, A]]
+[[Category: Wittinghofer A]]
-[[Category: Disease mutation]]
-[[Category: Gtp-binding]]
-[[Category: Gtpase activating protein and gtpase]]
-[[Category: Lipoprotein]]
-[[Category: Membrane]]
-[[Category: Metal binding protein]]
-[[Category: Myristate]]
-[[Category: Nucleotide-binding]]
-[[Category: Palmitate]]
-[[Category: Phosphoprotein]]
-[[Category: Protein-protein complex]]
-[[Category: Retinitis pigmentosa]]
-[[Category: Sensory transduction]]
-[[Category: Signaling protein]]
-[[Category: Vision]]

3bh6

From Proteopedia

Current revision

Crystal structure of the RP2-Arl3 complex bound to GppNHp

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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