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| - | [[Image:1egm.jpg|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K.== |
| - | |PDB= 1egm |SIZE=350|CAPTION= <scene name='initialview01'>1egm</scene>, resolution 1.85Å
| + | <StructureSection load='1egm' size='340' side='right'caption='[[1egm]], [[Resolution|resolution]] 1.85Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CNC:CO-CYANOCOBALAMIN'>CNC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PGO:1,2-PROPANEDIOL'>PGO</scene> | + | <table><tr><td colspan='2'>[[1egm]] 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=1EGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EGM FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[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] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CNC:CO-CYANOCOBALAMIN'>CNC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1egm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1egm OCA], [https://pdbe.org/1egm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1egm RCSB], [https://www.ebi.ac.uk/pdbsum/1egm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1egm ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1dio|1DIO]], [[1eex|1EEX]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1egm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1egm OCA], [http://www.ebi.ac.uk/pdbsum/1egm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1egm RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/Q59470_KLEOX Q59470_KLEOX] |
| - | | + | == Evolutionary Conservation == |
| - | '''CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K.'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eg/1egm_consurf.spt"</scriptWhenChecked> |
| - | 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.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1EGM is a [[Protein complex]] 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=1EGM OCA].
| + | </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=1egm ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | __TOC__ |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/10903944 10903944]
| + | </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: cyanocobalamin]]
| + | |
| - | [[Category: potassium ion]]
| + | |
| - | [[Category: propanediol]]
| + | |
| - | [[Category: tim barrel]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:02:09 2008''
| + | |
