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1s9a

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(New page: 200px<br /><applet load="1s9a" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s9a, resolution 2.47&Aring;" /> '''Crystal Structure of...)
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[[Image:1s9a.gif|left|200px]]<br /><applet load="1s9a" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1s9a, resolution 2.47&Aring;" />
 
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'''Crystal Structure of 4-Chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP'''<br />
 
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==Overview==
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==Crystal Structure of 4-Chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP==
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The crystal structure of the 4-chlorocatechol 1,2-dioxygenase from the, Gram-positive bacterium Rhodococcus opacus (erythropolis) 1CP, a Fe(III), ion-containing enzyme involved in the aerobic biodegradation of, chloroaromatic compounds, has been solved by multiple wavelength anomalous, dispersion using the weak anomalous signal of the two catalytic irons (1, Fe/257 amino acids) and refined at a 2.5 A resolution (R(free) 28.7%; R, factor 21.4%). The analysis of the structure and its comparison with the, structure of catechol 1,2-dioxygenase from Acinetobacter calcoaceticus, ADP1 (Ac 1,2-CTD) highlight significant differences between these enzymes., The general topology of the present enzyme comprises two catalytic domains, (one for each subunit) related by a noncrystallographic 2-fold axis and, separated by a common alpha-helical zipper motif consisting of five, N-terminal helices from each subunit; furthermore the C-terminal tail is, shortened significantly with respect to the known Ac 1,2-CTD. The presence, of two phospholipids binding in a hydrophobic tunnel along the dimer axis, is shown here to be a common feature for this class of enzyme. The active, site cavity presents several dissimilarities with respect to the known, catechol-cleaving enzyme. The catalytic nonheme iron(III) ion is bound to, the side chains of Tyr-134, Tyr-169, His-194, and His-196, and a, cocrystallized benzoate ion, bound to the metal center, reveals details on, a novel mode of binding of bidentate inhibitors and a distinctive hydrogen, bond network with the surrounding ligands. Among the amino acid residues, expected to interact with substrates, several are different from the, corresponding analogs of Ac 1,2-CTD: Asp-52, Ala-53, Gly-76, Phe-78, and, Cys-224; in addition, regions of largely conserved amino acid residues in, the catalytic cleft show different shapes resulting from several, substantial backbone and side chain shifts. The present structure is the, first of intradiol dioxygenases that specifically catalyze the cleavage of, chlorocatechols, key intermediates in the aerobic catabolism of toxic, chloroaromatics.
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<StructureSection load='1s9a' size='340' side='right'caption='[[1s9a]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1s9a]] 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=1S9A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S9A FirstGlance]. <br>
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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]] 2.47&#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=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HGP:(1-HEXADECANOYL-2-TETRADECANOYL-GLYCEROL-3-YL)+PHOSPHONYL+CHOLINE'>HGP</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></td></tr>
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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=1s9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9a OCA], [https://pdbe.org/1s9a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9a RCSB], [https://www.ebi.ac.uk/pdbsum/1s9a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9a ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CLCA_RHOOP CLCA_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/s9/1s9a_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=1s9a ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1S9A is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_opacus Rhodococcus opacus] with FE, HGP, TAM and BEZ as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Catechol_1,2-dioxygenase Catechol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.1 1.13.11.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S9A OCA].
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of 4-chlorocatechol 1,2-dioxygenase from the chlorophenol-utilizing gram-positive Rhodococcus opacus 1CP., Ferraroni M, Solyanikova IP, Kolomytseva MP, Scozzafava A, Golovleva L, Briganti F, J Biol Chem. 2004 Jun 25;279(26):27646-55. Epub 2004 Apr 1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15060064 15060064]
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[[Category: Large Structures]]
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[[Category: Catechol 1,2-dioxygenase]]
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[[Category: Rhodococcus opacus]]
[[Category: Rhodococcus opacus]]
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[[Category: Single protein]]
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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: Golovleva LA]]
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[[Category: Golovleva, L.A.]]
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[[Category: Kolomytseva MP]]
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[[Category: Kolomytseva, M.P.]]
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[[Category: Scozzafava A]]
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[[Category: Scozzafava, A.]]
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[[Category: Solyanikova IP]]
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[[Category: Solyanikova, I.P.]]
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[[Category: BEZ]]
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[[Category: FE]]
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[[Category: HGP]]
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[[Category: TAM]]
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[[Category: beta barrel]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:12:49 2007''
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Current revision

Crystal Structure of 4-Chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP

PDB ID 1s9a

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