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| | ==Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition== | | ==Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition== |
| - | <StructureSection load='1knf' size='340' side='right' caption='[[1knf]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='1knf' size='340' side='right'caption='[[1knf]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1knf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KNF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1knf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KNF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MBD:3-METHYLCATECHOL'>MBD</scene>, <scene name='pdbligand=TBU:TERTIARY-BUTYL+ALCOHOL'>TBU</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1han|1han]], [[1kmy|1kmy]], [[1knd|1knd]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MBD:3-METHYLCATECHOL'>MBD</scene>, <scene name='pdbligand=TBU:TERTIARY-BUTYL+ALCOHOL'>TBU</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BPHC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 Burkholderia cepacia LB400])</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=1knf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1knf OCA], [https://pdbe.org/1knf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1knf RCSB], [https://www.ebi.ac.uk/pdbsum/1knf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1knf ProSAT]</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=1knf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1knf OCA], [http://pdbe.org/1knf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1knf RCSB], [http://www.ebi.ac.uk/pdbsum/1knf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1knf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BPHC_BURXL BPHC_BURXL]] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents. | + | [https://www.uniprot.org/uniprot/BPHC_PARXL BPHC_PARXL] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1knf" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1knf" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Biphenyl-2,3-diol 1,2-dioxygenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Burkholderia cepacia lb400]] | + | [[Category: Paraburkholderia xenovorans LB400]] |
| - | [[Category: Bolin, J T]] | + | [[Category: Bolin JT]] |
| - | [[Category: Han, S]] | + | [[Category: Han S]] |
| - | [[Category: 3-dihydroxybiphenyl]]
| + | |
| - | [[Category: 3-methyl catechol]]
| + | |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
BPHC_PARXL Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.
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 PubMed
The steady-state cleavage of catechols by 2,3-dihydroxybiphenyl 1, 2-dioxygenase (DHBD), the extradiol dioxygenase of the biphenyl biodegradation pathway, was investigated using a highly active, anaerobically purified preparation of enzyme. The kinetic data obtained using 2,3-dihydroxybiphenyl (DHB) fit a compulsory order ternary complex mechanism in which substrate inhibition occurs. The Km for dioxygen was 1280 +/- 70 microM, which is at least 2 orders of magnitude higher than that reported for catechol 2,3-dioxygenases. Km and Kd for DHB were 22 +/- 2 and 8 +/- 1 microM, respectively. DHBD was subject to reversible substrate inhibition and mechanism-based inactivation. In air-saturated buffer, the partition ratios of catecholic substrates substituted at C-3 were inversely related to their apparent specificity constants. Small organic molecules that stabilized DHBD most effectively also inhibited the cleavage reaction most strongly. The steady-state kinetic data and crystallographic results suggest that the stabilization and inhibition are due to specific interactions between the organic molecule and the active site of the enzyme. t-Butanol stabilized the enzyme and inhibited the cleavage of DHB in a mixed fashion, consistent with the distinct binding sites occupied by t-butanol in the crystal structures of the substrate-free form of the enzyme and the enzyme-DHB complex. In contrast, crystal structures of complexes with catechol and 3-methylcatechol revealed relationships between the binding of these smaller substrates and t-butanol that are consistent with the observed competitive inhibition.
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.,Vaillancourt FH, Han S, Fortin PD, Bolin JT, Eltis LD J Biol Chem. 1998 Dec 25;273(52):34887-95. PMID:9857017[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Vaillancourt FH, Han S, Fortin PD, Bolin JT, Eltis LD. Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol. J Biol Chem. 1998 Dec 25;273(52):34887-95. PMID:9857017
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