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1r9d

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[[Image:1r9d.gif|left|200px]]
 
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{{Structure
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==Glycerol bound form of the B12-independent glycerol dehydratase from Clostridium butyricum==
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|PDB= 1r9d |SIZE=350|CAPTION= <scene name='initialview01'>1r9d</scene>, resolution 1.8&Aring;
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<StructureSection load='1r9d' size='340' side='right'caption='[[1r9d]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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<table><tr><td colspan='2'>[[1r9d]] 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=1R9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R9D FirstGlance]. <br>
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|ACTIVITY=
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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]] 1.8&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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}}
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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=1r9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9d OCA], [https://pdbe.org/1r9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r9d RCSB], [https://www.ebi.ac.uk/pdbsum/1r9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9d ProSAT]</span></td></tr>
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</table>
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'''Glycerol bound form of the B12-independent glycerol dehydratase from Clostridium butyricum'''
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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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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r9/1r9d_consurf.spt"</scriptWhenChecked>
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1R9D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_butyricum Clostridium butyricum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R9D OCA].
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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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==Reference==
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</jmolCheckbox>
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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://www.ncbi.nlm.nih.gov/pubmed/15096031 15096031]
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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=1r9d 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: GOL]]
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[[Category: glycerol dehydratase]]
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[[Category: radical sam]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:48:28 2008''
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Current revision

Glycerol bound form of the B12-independent glycerol dehydratase from Clostridium butyricum

PDB ID 1r9d

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