3o32: Difference between revisions
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< | ==Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with 3,5-dichlorocatechol== | ||
<StructureSection load='3o32' size='340' side='right'caption='[[3o32]], [[Resolution|resolution]] 2.85Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3o32]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_opacus Rhodococcus opacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O32 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]] 2.85Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=35C:3,5-DICHLOROBENZENE-1,2-DIOL'>35C</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MYY:(2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYL+PALMITATE'>MYY</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=3o32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o32 OCA], [https://pdbe.org/3o32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o32 RCSB], [https://www.ebi.ac.uk/pdbsum/3o32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o32 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CLCA_RHOOP CLCA_RHOOP] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystallographic structures of 4-chlorocatechol 1,2-dioxygenase (4-CCD) complexes with 3,5-dichlorocatechol, protocatechuate (3,4-dihydroxybenzoate), hydroxyquinol (benzen-1,2,4-triol) and pyrogallol (benzen-1,2,3-triol), which act as substrates or inhibitors of the enzyme, have been determined and analyzed. 4-CCD from the Gram-positive bacterium Rhodococcus opacus 1CP is a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of chlorocatechols. The structures of the 4-CCD complexes show that the catechols bind the catalytic iron ion in a bidentate mode displacing Tyr169 and the benzoate ion (found in the native enzyme structure) from the metal coordination sphere, as found in other adducts of intradiol dioxygenases with substrates. The analysis of the present structures allowed to identify the residues selectively involved in recognition of the diverse substrates. Furthermore the structural comparison with the corresponding complexes of catechol 1,2-dioxygenase from the same Rhodococcus strain (Rho-1,2-CTD) highlights significant differences in the binding of the tested catechols to the active site of the enzyme, particularly in the orientation of the aromatic ring substituents. As an example the 3-substituted catechols are bound with the substituent oriented towards the external part of the 4-CCD active site cavity, whereas in the Rho-1,2-CTD complexes the 3-substituents were placed in the internal position. The present crystallographic study shed light on the mechanism that allows substrate recognition inside this class of high specific enzymes involved in the biodegradation of recalcitrant pollutants. | |||
X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: new perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity.,Ferraroni M, Kolomytseva M, Scozzafava A, Golovleva L, Briganti F J Struct Biol. 2013 Mar;181(3):274-82. doi: 10.1016/j.jsb.2012.11.007. Epub 2012 , Dec 20. PMID:23261399<ref>PMID:23261399</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3o32" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
[[ | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Rhodococcus opacus]] | [[Category: Rhodococcus opacus]] | ||
[[Category: Briganti | [[Category: Briganti F]] | ||
[[Category: Ferraroni | [[Category: Ferraroni M]] | ||
[[Category: L | [[Category: Golovleva L]] | ||
[[Category: M | [[Category: Kolomytseva M]] | ||
Latest revision as of 12:26, 6 September 2023
Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with 3,5-dichlorocatecholCrystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex with 3,5-dichlorocatechol
Structural highlights
FunctionPublication Abstract from PubMedThe crystallographic structures of 4-chlorocatechol 1,2-dioxygenase (4-CCD) complexes with 3,5-dichlorocatechol, protocatechuate (3,4-dihydroxybenzoate), hydroxyquinol (benzen-1,2,4-triol) and pyrogallol (benzen-1,2,3-triol), which act as substrates or inhibitors of the enzyme, have been determined and analyzed. 4-CCD from the Gram-positive bacterium Rhodococcus opacus 1CP is a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of chlorocatechols. The structures of the 4-CCD complexes show that the catechols bind the catalytic iron ion in a bidentate mode displacing Tyr169 and the benzoate ion (found in the native enzyme structure) from the metal coordination sphere, as found in other adducts of intradiol dioxygenases with substrates. The analysis of the present structures allowed to identify the residues selectively involved in recognition of the diverse substrates. Furthermore the structural comparison with the corresponding complexes of catechol 1,2-dioxygenase from the same Rhodococcus strain (Rho-1,2-CTD) highlights significant differences in the binding of the tested catechols to the active site of the enzyme, particularly in the orientation of the aromatic ring substituents. As an example the 3-substituted catechols are bound with the substituent oriented towards the external part of the 4-CCD active site cavity, whereas in the Rho-1,2-CTD complexes the 3-substituents were placed in the internal position. The present crystallographic study shed light on the mechanism that allows substrate recognition inside this class of high specific enzymes involved in the biodegradation of recalcitrant pollutants. X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: new perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity.,Ferraroni M, Kolomytseva M, Scozzafava A, Golovleva L, Briganti F J Struct Biol. 2013 Mar;181(3):274-82. doi: 10.1016/j.jsb.2012.11.007. Epub 2012 , Dec 20. PMID:23261399[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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