3geh

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{{Seed}}
 
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[[Image:3geh.jpg|left|200px]]
 
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==Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN==
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The line below this paragraph, containing "STRUCTURE_3geh", creates the "Structure Box" on the page.
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<StructureSection load='3geh' size='340' side='right'caption='[[3geh]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3geh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc_sp._PCC_7120_=_FACHB-418 Nostoc sp. PCC 7120 = FACHB-418]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GEH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GEH FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 3.2&#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=FON:N-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC+ACID'>FON</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3geh| PDB=3geh | SCENE= }}
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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=3geh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3geh OCA], [https://pdbe.org/3geh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3geh RCSB], [https://www.ebi.ac.uk/pdbsum/3geh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3geh ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MNME_NOSS1 MNME_NOSS1] 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.[HAMAP-Rule:MF_00379]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/3geh_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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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=3geh ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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MnmE, which is involved in the modification of the wobble position of certain tRNAs, belongs to the expanding class of G proteins activated by nucleotide-dependent dimerization (GADs). Previous models suggested the protein to be a multidomain protein whose G domains contact each other in a nucleotide dependent manner. Here we employ a combined approach of X-ray crystallography and pulse electron paramagnetic resonance (EPR) spectroscopy to show that large domain movements are coupled to the G protein cycle of MnmE. The X-ray structures show MnmE to be a constitutive homodimer where the highly mobile G domains face each other in various orientations but are not in close contact as suggested by the GDP-AlF(x) structure of the isolated domains. Distance measurements by pulse double electron-electron resonance (DEER) spectroscopy show that the G domains adopt an open conformation in the nucleotide free/GDP-bound and an open/closed two-state equilibrium in the GTP-bound state, with maximal distance variations of 18 A. With GDP and AlF(x), which mimic the transition state of the phosphoryl transfer reaction, only the closed conformation is observed. Dimerization of the active sites with GDP-AlF(x) requires the presence of specific monovalent cations, thus reflecting the requirements for the GTPase reaction of MnmE. Our results directly demonstrate the nature of the conformational changes MnmE was previously suggested to undergo during its GTPase cycle. They show the nucleotide-dependent dynamic movements of the G domains around two swivel positions relative to the rest of the protein, and they are of crucial importance for understanding the mechanistic principles of this GAD.
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===Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN===
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Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy.,Meyer S, Bohme S, Kruger A, Steinhoff HJ, Klare JP, Wittinghofer A PLoS Biol. 2009 Oct;7(10):e1000212. Epub 2009 Oct 6. PMID:19806182<ref>PMID:19806182</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19806182}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3geh" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19806182 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19806182}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3GEH is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Nostoc_sp._pcc_7120 Nostoc sp. pcc 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GEH OCA].
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[[Category: Nostoc sp. PCC 7120 = FACHB-418]]
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[[Category: Meyer S]]
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==Reference==
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[[Category: Wittinghofer A]]
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<ref group="xtra">PMID:19806182</ref><references group="xtra"/>
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[[Category: Nostoc sp. pcc 7120]]
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[[Category: Meyer, S.]]
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[[Category: Wittinghofer, A.]]
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[[Category: Cytoplasm]]
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[[Category: G protein]]
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[[Category: Gtp-binding]]
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[[Category: Gtpase]]
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[[Category: Hydrolase]]
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[[Category: Magnesium]]
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[[Category: Metal-binding]]
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[[Category: Nucleotide-binding]]
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[[Category: Potassium]]
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[[Category: Trna modification]]
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[[Category: Trna processing]]
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[[Category: U34]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 28 13:29:24 2009''
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Current revision

Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN

PDB ID 3geh

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