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1eex

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[[Image:1eex.jpg|left|200px]]<br /><applet load="1eex" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1eex, resolution 1.7&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA==
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BACKGROUND: Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved. RESULTS: We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS: The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.
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<StructureSection load='1eex' size='340' side='right'caption='[[1eex]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1eex]] 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=1EEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EEX FirstGlance]. <br>
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1EEX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca] with <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=COY:'>COY</scene> and <scene name='pdbligand=PGO:'>PGO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EEX 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]] 1.7&#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=COY:CO-(ADENIN-9-YL-PENTYL)-COBALAMIN'>COY</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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==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=1eex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eex OCA], [https://pdbe.org/1eex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eex RCSB], [https://www.ebi.ac.uk/pdbsum/1eex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eex ProSAT]</span></td></tr>
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How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex., Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N, Structure. 2000 Jul 15;8(7):775-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10903944 10903944]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q59470_KLEOX Q59470_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/ee/1eex_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=1eex ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[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: Protein complex]]
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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: 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: COY]]
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[[Category: K]]
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[[Category: PGO]]
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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 Thu Feb 21 12:26:59 2008''
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Current revision

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

PDB ID 1eex

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