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1r8w

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(New page: 200px<br /><applet load="1r8w" size="450" color="white" frame="true" align="right" spinBox="true" caption="1r8w, resolution 2.50&Aring;" /> '''Native structure of ...)
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[[Image:1r8w.jpg|left|200px]]<br /><applet load="1r8w" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1r8w, resolution 2.50&Aring;" />
 
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'''Native structure of the B12-independent glycerol dehydratase from clostridium butyricum'''<br />
 
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==Overview==
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==Native structure of the B12-independent glycerol dehydratase from clostridium butyricum==
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The molecular characterization of a B12-independent glycerol dehydratase, from Clostridium butyricum has recently been reported [Raynaud, C., et al., (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 5010-5015]. In this work, we, have further characterized this system by biochemical and crystallographic, methods. Both the glycerol dehydratase (GD) and the GD-activating enzyme, (GD-AE) could be purified to homogeneity under aerobic conditions. In this, form, both the GD and GD-AE were inactive. A reconstitution procedure, similar to what has been reported for pyruvate formate lyase activating, enzyme (PFL-AE), was employed to reconstitute the activity of the GD-AE., Subsequently, the reconstituted GD-AE could be used to reactivate the GD, under strictly anaerobic conditions. We also report here the crystal, structure of the inactive GD in the native (2.5 A resolution, Rcryst =, 17%, Rfree = 20%), glycerol-bound (1.8 A resolution, Rcryst = 21%, Rfree =, 24%), and 1,2-propanediol-bound (2.4 A resolution, Rcryst = 20%, Rfree =, 24%) forms. The overall fold of the GD monomer was similar to what has, been observed for pyruvate formate lyase (PFL) and anaerobic, ribonucleotide reductase (ARNR), consisting of a 10-stranded beta/alpha, barrel motif. Clear density was observed for both substrates, and a, mechanism for the dehydration reaction is presented. This mechanism, clearly supports a concerted pathway for migration of the OH group through, a cyclic transition state that is stabilized by partial protonation of the, migrating OH group. Finally, despite poor alignment (rmsd approximately, 6.8 A) of the 10 core strands that comprise the barrel structure of the GD, and PFL, the C-terminal domains of both proteins align well (rmsd, approximately 0.7 A) and have structural properties consistent with this, being the docking site for the activating enzyme. A single point mutation, within this domain, at a strictly conserved arginine residue (R782K) in, the GD, resulted in formation of a tight protein-protein complex between, the GD and the GD-AE in vivo, thereby supporting this hypothesis.
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<StructureSection load='1r8w' size='340' side='right'caption='[[1r8w]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1r8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_butyricum Clostridium butyricum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R8W FirstGlance]. <br>
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1R8W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_butyricum Clostridium butyricum]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R8W 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]] 2.5&#8491;</td></tr>
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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=1r8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r8w OCA], [https://pdbe.org/1r8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r8w RCSB], [https://www.ebi.ac.uk/pdbsum/1r8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r8w ProSAT]</span></td></tr>
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==Reference==
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</table>
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Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization., O'Brien JR, Raynaud C, Croux C, Girbal L, Soucaille P, Lanzilotta WN, Biochemistry. 2004 Apr 27;43(16):4635-45. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15096031 15096031]
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== Function ==
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[https://www.uniprot.org/uniprot/Q8GEZ8_CLOBU Q8GEZ8_CLOBU]
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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/r8/1r8w_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=1r8w ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Clostridium butyricum]]
[[Category: Clostridium butyricum]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Brien, J.R.O.]]
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[[Category: Lanzilotta WN]]
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[[Category: Lanzilotta, W.N.]]
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[[Category: O'Brien JR]]
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[[Category: Raynaud, C.]]
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[[Category: Raynaud C]]
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[[Category: Soucaille, P.]]
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[[Category: Soucaille P]]
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[[Category: glycerol dehydratase]]
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[[Category: radical sam]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:22:24 2007''
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Current revision

Native structure of the B12-independent glycerol dehydratase from clostridium butyricum

PDB ID 1r8w

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