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| ==Crystal structure of LepB GAP domain from Legionella drancourtii in complex with Rab1-GDP and AlF3== | | ==Crystal structure of LepB GAP domain from Legionella drancourtii in complex with Rab1-GDP and AlF3== |
| <StructureSection load='4jvs' size='340' side='right' caption='[[4jvs]], [[Resolution|resolution]] 2.78Å' scene=''> | | <StructureSection load='4jvs' size='340' side='right'caption='[[4jvs]], [[Resolution|resolution]] 2.78Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4jvs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Legionella_drancourtii_llap12 Legionella drancourtii llap12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JVS FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4jvs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Legionella_drancourtii_LLAP12 Legionella drancourtii LLAP12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JVS FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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]] 2.783Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jw1|4jw1]]</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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">LDG_7216 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=658187 Legionella drancourtii LLAP12]), RAB1A ([http://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=4jvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jvs OCA], [https://pdbe.org/4jvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jvs RCSB], [https://www.ebi.ac.uk/pdbsum/4jvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jvs 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=4jvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jvs OCA], [http://pdbe.org/4jvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jvs RCSB], [http://www.ebi.ac.uk/pdbsum/4jvs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jvs ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RAB1A_HUMAN RAB1A_HUMAN]] Probably required for transit of protein from the ER through Golgi compartment. Binds GTP and GDP and possesses intrinsic GTPase activity. | | [https://www.uniprot.org/uniprot/G9EPL4_9GAMM G9EPL4_9GAMM] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Rab GTPases are emerging targets of diverse bacterial pathogens. Here, we perform biochemical and structural analyses of LepB, a Rab GTPase-activating protein (GAP) effector from Legionella pneumophila. We map LepB GAP domain to residues 313-618 and show that the GAP domain is Rab1 specific with a catalytic activity higher than the canonical eukaryotic TBC GAP and the newly identified VirA/EspG family of bacterial RabGAP effectors. Exhaustive mutation analyses identify Arg444 as the arginine finger, but no catalytically essential glutamine residues. Crystal structures of LepB313-618 alone and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AlF3 support the catalytic role of Arg444, and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs. Glu449, structurally equivalent to TBC RabGAP glutamine finger in apo-LepB, undergoes a drastic movement upon Rab1 binding, which induces Rab1 Gln70 side-chain flipping towards GDP-AlF3 through a strong ionic interaction. This conformationally rearranged Gln70 acts as the catalytic cis-glutamine, therefore uncovering an unexpected RasGAP-like catalytic mechanism for LepB. Our studies highlight an extraordinary structural and catalytic diversity of RabGAPs, particularly those from bacterial pathogens.Cell Research advance online publication 16 April 2013; doi:10.1038/cr.2013.54.
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| Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP.,Yu Q, Hu L, Yao Q, Zhu Y, Dong N, Wang DC, Shao F Cell Res. 2013 Apr 16. doi: 10.1038/cr.2013.54. PMID:23588383<ref>PMID:23588383</ref>
| | ==See Also== |
| | | *[[Ras-related protein Rab 3D structures|Ras-related protein Rab 3D structures]] |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4jvs" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Human]] | | [[Category: Homo sapiens]] |
| [[Category: Legionella drancourtii llap12]] | | [[Category: Large Structures]] |
| [[Category: Shao, F]] | | [[Category: Legionella drancourtii LLAP12]] |
| [[Category: Wang, D C]] | | [[Category: Shao F]] |
| [[Category: Yao, Q]] | | [[Category: Wang D-C]] |
| [[Category: Yu, Q]] | | [[Category: Yao Q]] |
| [[Category: Bind and hydrolyze guanosine triphosphate]]
| | [[Category: Yu Q]] |
| [[Category: Hydrolase activator-protein transport complex]]
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| [[Category: New gap fold]]
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| [[Category: Rab1 binding]]
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