3q08

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<StructureSection load='3q08' size='340' side='right'caption='[[3q08]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
<StructureSection load='3q08' size='340' side='right'caption='[[3q08]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q08]] 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=3m2q 3m2q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q08 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q08]] 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=3m2q 3m2q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q08 FirstGlance]. <br>
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</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
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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]] 3.05&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q09|3q09]]</div></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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
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<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>
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<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>
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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=3q08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q08 OCA], [https://pdbe.org/3q08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q08 RCSB], [https://www.ebi.ac.uk/pdbsum/3q08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q08 ProSAT]</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=3q08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q08 OCA], [https://pdbe.org/3q08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q08 RCSB], [https://www.ebi.ac.uk/pdbsum/3q08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q08 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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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 3q08" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Decar]]
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[[Category: Dechloromonas aromatica RCB]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Goblirsch, B R]]
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[[Category: Goblirsch BR]]
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[[Category: Wilmot, C M]]
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[[Category: Wilmot CM]]
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[[Category: Chlorite decomposition]]
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[[Category: Ferrodoxin fold]]
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[[Category: O2 generation]]
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[[Category: Oxidoreductase]]
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[[Category: Periplasim]]
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Current revision

Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 6.5

PDB ID 3q08

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