3hj8

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{{Seed}}
 
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[[Image:3hj8.jpg|left|200px]]
 
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==Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 4-chlorocatechol==
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The line below this paragraph, containing "STRUCTURE_3hj8", creates the "Structure Box" on the page.
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<StructureSection load='3hj8' size='340' side='right'caption='[[3hj8]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3hj8]] is a 1 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=3HJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HJ8 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4CL:4-CHLOROBENZENE-1,2-DIOL'>4CL</scene>, <scene name='pdbligand=6PL:(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM+4-OXIDE'>6PL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
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{{STRUCTURE_3hj8| PDB=3hj8 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hj8 OCA], [https://pdbe.org/3hj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hj8 RCSB], [https://www.ebi.ac.uk/pdbsum/3hj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hj8 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CATA_RHOOP CATA_RHOOP]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hj/3hj8_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3hj8 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The first crystallographic structures of a catechol 1,2-dioxygenase from a Gram-positive bacterium Rhodococcus opacus 1CP (Rho 1,2-CTD), a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of catechols, and its adducts with catechol, 3-methylcatechol, 4-methylcatechol, pyrogallol (benzene-1,2,3-triol), 3-chlorocatechol, 4-chlorocatechol, 3,5-dichlorocatechol, 4,5-dichlorocatechol and protocatechuate (3,4-dihydroxybenzoate) have been determined and analyzed. This study represents the first extensive characterization of catechols adducts of 1,2-CTDs. The structural analyses reveal the diverse modes of binding to the active metal iron ion of the tested catechols thus allowing to identify the residues selectively involved in recognition of the diverse substrates by this class of enzymes. The comparison is further extended to the structural and functional characteristics of the other 1,2-CTDs isolated from Gram-positive and Gram-negative bacteria. Moreover the high structural homology of the present enzyme with the 3-chlorocatechol 1,2-dioxygenase from the same bacterium are discussed in terms of their different substrate specificity. The catalytic rates for Rho 1,2-CTD conversion of the tested compounds are also compared with the calculated energies of the highest occupied molecular orbital (E(HOMO)) of the substrates. A quantitative relationship (R=0.966) between the ln k(cat) and the calculated electronic parameter E(HOMO) was obtained for catechol, 3-methylcatechol, 4-methylcatechol, pyrogallol, 3-chlorocatechol, 4-chlorocatechol. This indicates that for these substrates the rate-limiting step of the reaction cycle is dependent on their nucleophilic reactivity. The discrepancies observed in the quantitative relationship for 3,5-dichlorocatechol, 4,5-dichlorocatechol and protocatechuate are ascribed to the sterical hindrances leading to the distorted binding of such catechols observed in the corresponding structures.
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===Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 4-chlorocatechol===
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Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts.,Matera I, Ferraroni M, Kolomytseva M, Golovleva L, Scozzafava A, Briganti F J Struct Biol. 2010 Jun;170(3):548-64. Epub 2009 Dec 28. PMID:20040374<ref>PMID:20040374</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3hj8" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20040374}}, adds the Publication Abstract to the page
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 20040374 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20040374}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3HJ8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_opacus Rhodococcus opacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HJ8 OCA].
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==Reference==
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<ref group="xtra">PMID:20040374</ref><references group="xtra"/>
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[[Category: Catechol 1,2-dioxygenase]]
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[[Category: Rhodococcus opacus]]
[[Category: Rhodococcus opacus]]
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[[Category: Briganti, F.]]
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[[Category: Briganti F]]
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[[Category: Ferraroni, M.]]
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[[Category: Ferraroni M]]
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[[Category: Matera, I.]]
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[[Category: Matera I]]
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[[Category: Scozzafava, A.]]
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[[Category: Scozzafava A]]
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[[Category: Aromatic hydrocarbons catabolism]]
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[[Category: Beta-sandwich]]
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[[Category: Dioxygenase]]
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[[Category: Iron]]
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[[Category: Metal-binding]]
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[[Category: Oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 13 14:12:51 2010''
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Current revision

Crystal structure determination of catechol 1,2-dioxygenase from rhodococcus opacus 1CP in complex with 4-chlorocatechol

PDB ID 3hj8

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