1kw3: Difference between revisions
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==Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution== | ==Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution== | ||
<StructureSection load='1kw3' size='340' side='right' caption='[[1kw3]], [[Resolution|resolution]] 1.45Å' scene=''> | <StructureSection load='1kw3' size='340' side='right' caption='[[1kw3]], [[Resolution|resolution]] 1.45Å' scene=''> | ||
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dhy|1dhy]], [[1eil|1eil]], [[1eiq|1eiq]], [[1kw6|1kw6]], [[1kw8|1kw8]], [[1kw9|1kw9]], [[1kwb|1kwb]], [[1kwc|1kwc]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dhy|1dhy]], [[1eil|1eil]], [[1eiq|1eiq]], [[1kw6|1kw6]], [[1kw8|1kw8]], [[1kw9|1kw9]], [[1kwb|1kwb]], [[1kwc|1kwc]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kw3 OCA], [http://pdbe.org/1kw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kw3 PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kw3 OCA], [http://pdbe.org/1kw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kw3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kw3_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kw3_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 1kw3" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 1kw3" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 00:37, 25 January 2018
Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolutionCrystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedBphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs) in the microbe. To elucidate detailed structures of BphC reaction intermediates, crystal structures of the substrate-free form, the BphC-substrate complex, and the BphC-substrate-NO (nitric oxide) complex were determined. These crystal structures revealed (1) the binding site of the O(2) molecule in the coordination sphere and (2) conformational changes of His194 during the catalytic reaction. On the basis of these findings, we propose a catalytic mechanism for the extradiol-cleaving catecholic dioxygenase in which His194 seems to play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. At the next stage, the protonated His194 seems to stabilize a negative charge on the O2 molecule located in the hydrophobic O2-binding cavity. Finally, protonated His194 seems to function as a proton donor, whose existence has been proposed. Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase.,Sato N, Uragami Y, Nishizaki T, Takahashi Y, Sazaki G, Sugimoto K, Nonaka T, Masai E, Fukuda M, Senda T J Mol Biol. 2002 Aug 23;321(4):621-36. PMID:12206778[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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