2gj9

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[[Image:2gj9.gif|left|200px]]<br /><applet load="2gj9" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2gj9, resolution 2.000&Aring;" />
 
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'''Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+'''<br />
 
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==Overview==
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==Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+==
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MnmE, a Guanine nucleotide-binding protein conserved between bacteria and man, is involved in the modification of tRNAs. Here we provide biochemical and X-ray structural evidence for a new GTP-hydrolysis mechanism, where the G-domains of MnmE dimerise in a potassium-dependent manner and induce GTP hydrolysis. The structure in the presence of GDP-AlFx and potassium shows how juxtaposition of the subunits induces a conformational change around the nucleotide which reorients the catalytic machinery. A critical glutamate is positioned such as to stabilise or activate the attacking water. Potassium provides a positive charge into the catalytic site in a position analogous to the arginine finger in the Ras-RasGAP system. Mutational studies show that potassium-dependent dimerisation and GTP hydrolysis can be uncoupled and that interaction between the G-domains is a prerequisite for subsequent phosphoryl transfer. We propose a model for the juxtaposition of G-domains in the full-length protein and how it induces conformational changes in the putative tRNA-modification centre.
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<StructureSection load='2gj9' size='340' side='right'caption='[[2gj9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2gj9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GJ9 FirstGlance]. <br>
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2GJ9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ALF:'>ALF</scene>, <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=RB:'>RB</scene> and <scene name='pdbligand=GDP:'>GDP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJ9 OCA].
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</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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gj9 OCA], [https://pdbe.org/2gj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gj9 RCSB], [https://www.ebi.ac.uk/pdbsum/2gj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gj9 ProSAT]</span></td></tr>
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Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element., Scrima A, Wittinghofer A, EMBO J. 2006 Jun 21;25(12):2940-51. Epub 2006 Jun 8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16763562 16763562]
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</table>
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[[Category: Escherichia coli]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/MNME_ECOLI MNME_ECOLI] Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34.
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[[Category: Scrima, A.]]
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== Evolutionary Conservation ==
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[[Category: Wittinghofer, A.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: ALF]]
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Check<jmol>
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[[Category: GDP]]
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<jmolCheckbox>
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[[Category: MG]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gj/2gj9_consurf.spt"</scriptWhenChecked>
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[[Category: RB]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: alpha-beta-sandwich]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: g-domain dimer]]
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2gj9 ConSurf].
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:32:13 2008''
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Scrima A]]
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[[Category: Wittinghofer A]]

Current revision

Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+

PDB ID 2gj9

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