2boy: Difference between revisions

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-[[Image:2boy.png|left|200px]]
-<!--
+==Crystal structure of 3-ChloroCatechol 1,2-Dioxygenase from Rhodococcus Opacus 1CP==
-The line below this paragraph, containing "STRUCTURE_2boy", creates the "Structure Box" on the page.
+<StructureSection load='2boy' size='340' side='right'caption='[[2boy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2boy]] is a 8 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=2BOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BOY FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BHO:BENZHYDROXAMIC+ACID'>BHO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LPP:2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2boy|  PDB=2boy  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2boy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2boy OCA], [https://pdbe.org/2boy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2boy RCSB], [https://www.ebi.ac.uk/pdbsum/2boy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2boy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8G9L3_RHOOP Q8G9L3_RHOOP]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bo/2boy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2boy ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the 3-chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium Rhodococcus opacus (erythropolis) 1CP, a Fe(III) ion-containing enzyme specialized in the aerobic biodegradation of 3-chloro- and methyl-substituted catechols, has been solved by molecular replacement techniques using the coordinates of 4-chlorocatechol 1,2-dioxygenase from the same organism (PDB code 1S9A) as a starting model and refined at 1.9 A resolution (R(free) 21.9%; R-factor 17.4%). The analysis of the structure and of the kinetic parameters for a series of different substrates, and the comparison with the corresponding data for the 4-chlorocatechol 1,2-dioxygenase isolated from the same bacterial strain, provides evidence of which active site residues are responsible for the observed differences in substrate specificity. Among the amino acid residues expected to interact with substrates, only three are altered Val53(Ala53), Tyr78(Phe78) and Ala221(Cys224) (3-chlorocatechol 1,2-dioxygenase(4-chlorocatechol 1,2-dioxygenase)), clearly identifying the substitutions influencing substrate selectivity in these enzymes. The crystallographic asymmetric unit contains eight subunits (corresponding to four dimers) that show heterogeneity in the conformation of a co-crystallized molecule bound to the catalytic non-heme iron(III) ion resembling a benzohydroxamate moiety, probably a result of the breakdown of recently discovered siderophores synthesized by Gram-positive bacteria. Several different modes of binding benzohydroxamate into the active site induce distinct conformations of the interacting protein ligands Tyr167 and Arg188, illustrating the plasticity of the active site origin of the more promiscuous substrate preferences of the present enzyme.
-===CRYSTAL STRUCTURE OF 3-CHLOROCATECHOL 1,2-DIOXYGENASE FROM RHODOCOCCUS OPACUS 1CP===
+Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol.,Ferraroni M, Kolomytseva MP, Solyanikova IP, Scozzafava A, Golovleva LA, Briganti F J Mol Biol. 2006 Jul 21;360(4):788-99. Epub 2006 Jun 5. PMID:16793061<ref>PMID:16793061</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2boy" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16793061}}, adds the Publication Abstract to the page
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16793061 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16793061}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2boy]] is a 8 chain structure with 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=2BOY OCA].
-==Reference==
-<ref group="xtra">PMID:16793061</ref><ref group="xtra">PMID:12499567</ref><references group="xtra"/>
-[[Category: Catechol 1,2-dioxygenase]]
 [[Category: Rhodococcus opacus]]
-[[Category: Briganti, F.]]
+[[Category: Briganti F]]
-[[Category: Ferraroni, M.]]
+[[Category: Ferraroni M]]
-[[Category: Golovleva, L A.]]
+[[Category: Golovleva LA]]
-[[Category: Kolomytseva, M P.]]
+[[Category: Kolomytseva MP]]
-[[Category: Scozzafava, A.]]
+[[Category: Scozzafava A]]
-[[Category: Solyanikova, I P.]]
+[[Category: Solyanikova IP]]
-[[Category: Beta barrel]]
-[[Category: Dioxygenase]]
-[[Category: Oxidoreductase]]