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New page: left|200px<br /><applet load="1eex" size="450" color="white" frame="true" align="right" spinBox="true" caption="1eex, resolution 1.7Å" /> '''CRYSTAL STRUCTURE OF ...
 
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[[Image:1eex.jpg|left|200px]]<br /><applet load="1eex" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1eex, resolution 1.7&Aring;" />
'''CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA'''<br />


==Overview==
==CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA==
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.
<StructureSection load='1eex' size='340' side='right'caption='[[1eex]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q59470_KLEOX Q59470_KLEOX]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ee/1eex_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==About this Structure==
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:10903944<ref>PMID:10903944</ref>
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 K, COY and PGO 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EEX OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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]
</div>
<div class="pdbe-citations 1eex" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Klebsiella oxytoca]]
[[Category: Klebsiella oxytoca]]
[[Category: Propanediol dehydratase]]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Masuda J]]
[[Category: Masuda, J.]]
[[Category: Morimoto Y]]
[[Category: Morimoto, Y.]]
[[Category: Shibata N]]
[[Category: Shibata, N.]]
[[Category: Toraya T]]
[[Category: Toraya, T.]]
[[Category: Yasuoka N]]
[[Category: Yasuoka, N.]]
[[Category: COY]]
[[Category: K]]
[[Category: PGO]]
[[Category: coenzyme b12]]
[[Category: potassium ion]]
[[Category: propanediol]]
[[Category: tim barrel]]
 
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Retrieved from "https://proteopedia.org/1eex"