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| | ==ARA7-GDP-Ca2+/VPS9a== | | ==ARA7-GDP-Ca2+/VPS9a== |
| - | <StructureSection load='4g01' size='340' side='right' caption='[[4g01]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='4g01' size='340' side='right'caption='[[4g01]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4g01]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [http://en.wikipedia.org/wiki/Zasmidium_angulare Zasmidium angulare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G01 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4g01]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G01 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2efc|2efc]], [[2efd|2efd]], [[2efe|2efe]], [[2efh|2efh]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VPS9A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]), ARA-7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1194242 Zasmidium angulare])</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=4g01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g01 OCA], [https://pdbe.org/4g01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g01 RCSB], [https://www.ebi.ac.uk/pdbsum/4g01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g01 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=4g01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g01 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g01 RCSB], [http://www.ebi.ac.uk/pdbsum/4g01 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> [[http://www.uniprot.org/uniprot/RAF2B_ARATH RAF2B_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref> | + | [https://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4g01" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Arabidopsis thaliana]] | | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Zasmidium angulare]] | + | [[Category: Large Structures]] |
| - | [[Category: Ihara, K]] | + | [[Category: Ihara K]] |
| - | [[Category: Divalent metal binding]]
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| - | [[Category: Gdp/gtp binding]]
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| - | [[Category: Geranylgeranylation]]
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| - | [[Category: Gtpase-gdp-metal-gef complex]]
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| - | [[Category: Guanine nucleotide exchange factor]]
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| - | [[Category: Ras super family]]
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| - | [[Category: Small gtpase]]
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| - | [[Category: Transport protein]]
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| - | [[Category: Vps9 domain]]
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| Structural highlights
Function
VPS9A_ARATH Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.[1] [2]
Publication Abstract from PubMed
Rab small GTPases regulate vesicle transport in eukaryotes by interacting with various effectors. Guanine nucleotide-exchange factor (GEF) catalyzes the transition from inactive GDP-bound Rab to active GTP-bound Rab. The existence of several GDP-bound intermediates containing the Arabidopsis thaliana Rab5 homologue ARA7 and the GEF VPS9a prior to the formation of a nucleotide-free binary complex has been proposed [Uejima et al. (2010), J. Biol. Chem. 285, 36689-36697]. During this process, VPS9a directly interacts with the beta-phosphate of GDP and the P-loop lysine of ARA7 via a catalytically important aspartate finger, which promotes the release of GDP from ARA7. However, it is unclear how VPS9a removes Mg2+ from ARA7 before forming the GDP-bound ternary complex. Here, the structure of the ARA7-GDP-Ca2+-VPS9a complex is reported, in which the aspartate finger directly coordinates the divalent metal ion. Ca2+ is bound to the canonical Mg2+-binding site, coordinated by the beta-phosphate of GDP and the P-loop serine of ARA7. Unexpectedly, Ca2+ is further coordinated by the aspartate finger and the main chain of VPS9a. This structure may represent the earliest intermediate step in the GEF-catalyzed nucleotide-exchange reaction of ARA7 before the metal-free GDP-bound intermediates are created.
Direct metal recognition by guanine nucleotide-exchange factor in the initial step of the exchange reaction.,Uejima T, Ihara K, Sunada M, Kawasaki M, Ueda T, Kato R, Nakano A, Wakatsuki S Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):345-51. doi:, 10.1107/S0907444912047294. Epub 2013 Feb 16. PMID:23519409[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Goh T, Uchida W, Arakawa S, Ito E, Dainobu T, Ebine K, Takeuchi M, Sato K, Ueda T, Nakano A. VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana. Plant Cell. 2007 Nov;19(11):3504-15. Epub 2007 Nov 30. PMID:18055610 doi:10.1105/tpc.107.053876
- ↑ Uejima T, Ihara K, Goh T, Ito E, Sunada M, Ueda T, Nakano A, Wakatsuki S. GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system. J Biol Chem. 2010 Nov 19;285(47):36689-97. Epub 2010 Sep 10. PMID:20833725 doi:10.1074/jbc.M110.152132
- ↑ Uejima T, Ihara K, Sunada M, Kawasaki M, Ueda T, Kato R, Nakano A, Wakatsuki S. Direct metal recognition by guanine nucleotide-exchange factor in the initial step of the exchange reaction. Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):345-51. doi:, 10.1107/S0907444912047294. Epub 2013 Feb 16. PMID:23519409 doi:10.1107/S0907444912047294
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