1dio

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{{Seed}}
 
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[[Image:1dio.png|left|200px]]
 
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==DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA==
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The line below this paragraph, containing "STRUCTURE_1dio", creates the "Structure Box" on the page.
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<StructureSection load='1dio' size='340' side='right'caption='[[1dio]], [[Resolution|resolution]] 2.20&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'>[[1dio]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DIO 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]] 2.2&#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=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
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{{STRUCTURE_1dio| PDB=1dio | 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=1dio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dio OCA], [https://pdbe.org/1dio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dio RCSB], [https://www.ebi.ac.uk/pdbsum/1dio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dio ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q59472_KLEOX Q59472_KLEOX]
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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/di/1dio_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=1dio 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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BACKGROUND: Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin (coenzyme B12) dependent conversion of 1,2-diols to the corresponding aldehydes. The reaction initiated by homolytic cleavage of the cobalt-carbon bond of the coenzyme proceeds by a radical mechanism. The enzyme is an alpha2beta2gamma2 heterooligomer and has an absolute requirement for a potassium ion for catalytic activity. The crystal structure analysis of a diol dehydratase-cyanocobalamin complex was carried out in order to help understand the mechanism of action of this enzyme. RESULTS: The three-dimensional structure of diol dehydratase in complex with cyanocobalamin was determined at 2.2 A resolution. The enzyme exists as a dimer of heterotrimers (alphabetagamma)2. The cobalamin molecule is bound between the alpha and beta subunits in the 'base-on' mode, that is, 5,6-dimethylbenzimidazole of the nucleotide moiety coordinates to the cobalt atom in the lower axial position. The alpha subunit includes a (beta/alpha)8 barrel. The substrate, 1,2-propanediol, and an essential potassium ion are deeply buried inside the barrel. The two hydroxyl groups of the substrate coordinate directly to the potassium ion. CONCLUSIONS: This is the first crystallographic indication of the 'base-on' mode of cobalamin binding. An unusually long cobalt-base bond seems to favor homolytic cleavage of the cobalt-carbon bond and therefore to favor radical enzyme catalysis. Reactive radical intermediates can be protected from side reactions by spatial isolation inside the barrel. On the basis of unique direct interactions between the potassium ion and the two hydroxyl groups of the substrate, direct participation of a potassium ion in enzyme catalysis is strongly suggested.
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===DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA===
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A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.,Shibata N, Masuda J, Tobimatsu T, Toraya T, Suto K, Morimoto Y, Yasuoka N Structure. 1999 Aug 15;7(8):997-1008. PMID:10467140<ref>PMID:10467140</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_10467140}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1dio" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 10467140 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_10467140}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1DIO is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DIO OCA].
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==Reference==
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<ref group="xtra">PMID:10467140</ref><references group="xtra"/>
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[[Category: Klebsiella oxytoca]]
[[Category: Klebsiella oxytoca]]
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[[Category: Propanediol dehydratase]]
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[[Category: Large Structures]]
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[[Category: Masuda, J.]]
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[[Category: Masuda J]]
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[[Category: Morimoto, Y.]]
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[[Category: Morimoto Y]]
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[[Category: Shibata, N.]]
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[[Category: Shibata N]]
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[[Category: Suto, K.]]
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[[Category: Suto K]]
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[[Category: Tobimatsu, T.]]
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[[Category: Tobimatsu T]]
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[[Category: Toraya, T.]]
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[[Category: Toraya T]]
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[[Category: Yasuoka, N.]]
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[[Category: Yasuoka N]]
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[[Category: Coenzyme b12]]
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[[Category: Potassium ion]]
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[[Category: Propanediol]]
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[[Category: Tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:54:00 2009''
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Current revision

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

PDB ID 1dio

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