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3q09

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Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 9.0

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Retrieved from "http://52.214.119.220/wiki/index.php/3q09"

Categories: Dechloromonas aromatica RCB | Large Structures | Goblirsch BR | Wilmot CM

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 <StructureSection load='3q09' size='340' side='right'caption='[[3q09]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3q09]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Decar Decar]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3m2s 3m2s]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q09 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3q09]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Dechloromonas_aromatica_RCB Dechloromonas aromatica RCB]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3m2s 3m2s]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q09 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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]] 3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q08|3q08]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Daro_2580 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=159087 DECAR])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chlorite_O(2)-lyase Chlorite O(2)-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.49 1.13.11.49] </span></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=3q09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q09 OCA], [https://pdbe.org/3q09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q09 RCSB], [https://www.ebi.ac.uk/pdbsum/3q09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q09 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CLD_DECAR CLD_DECAR]] Catalyzes the heme-dependent decomposition of chlorite to O(2) and chloride with high efficiency and specificity. Used to detoxify chlorite, a by-product of the reduction of perchlorate, a primarily anthropogenic pollutant, in perchlorate-respiring bacteria.<ref>PMID:18422344</ref>
+[https://www.uniprot.org/uniprot/CLD_DECAR CLD_DECAR] Catalyzes the heme-dependent decomposition of chlorite to O(2) and chloride with high efficiency and specificity. Used to detoxify chlorite, a by-product of the reduction of perchlorate, a primarily anthropogenic pollutant, in perchlorate-respiring bacteria.<ref>PMID:18422344</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Chlorite dismutase (Cld) is a heme enzyme capable of rapidly and selectively decomposing chlorite (ClO(2) (-)) to Cl(-) and O(2). The ability of Cld to promote O(2) formation from ClO(2) (-) is unusual. Heme enzymes generally utilize ClO(2) (-) as an oxidant for reactions such as oxygen atom transfer to, or halogenation of, a second substrate. The X-ray crystal structure of Dechloromonas aromatica Cld co-crystallized with the substrate analogue nitrite (NO(2) (-)) was determined to investigate features responsible for this novel reactivity. The enzyme active site contains a single b-type heme coordinated by a proximal histidine residue. Structural analysis identified a glutamate residue hydrogen-bonded to the heme proximal histidine that may stabilize reactive heme species. A solvent-exposed arginine residue likely gates substrate entry to a tightly confined distal pocket. On the basis of the proposed mechanism of Cld, initial reaction of ClO(2) (-) within the distal pocket generates hypochlorite (ClO(-)) and a compound I intermediate. The sterically restrictive distal pocket probably facilitates the rapid rebound of ClO(-) with compound I forming the Cl(-) and O(2) products. Common to other heme enzymes, Cld is inactivated after a finite number of turnovers, potentially via the observed formation of an off-pathway tryptophanyl radical species through electron migration to compound I. Three tryptophan residues of Cld have been identified as candidates for this off-pathway radical. Finally, a juxtaposition of hydrophobic residues between the distal pocket and the enzyme surface suggests O(2) may have a preferential direction for exiting the active site.
-Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase.,Goblirsch BR, Streit BR, Dubois JL, Wilmot CM J Biol Inorg Chem. 2010 Apr 13. PMID:20386942<ref>PMID:20386942</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3q09" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Decar]]
+[[Category: Dechloromonas aromatica RCB]]
 [[Category: Large Structures]]
-[[Category: Goblirsch, B R]]
+[[Category: Goblirsch BR]]
-[[Category: Wilmot, C M]]
+[[Category: Wilmot CM]]
-[[Category: Chlorite decomposition]]
-[[Category: Ferrodoxin fold]]
-[[Category: O2 generation]]
-[[Category: Oxidoreductase]]
-[[Category: Periplasim]]

3q09

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Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 9.0

Structural highlights

Function

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