3q09: Difference between revisions

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== Structural highlights ==

<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>

<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]. 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</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>

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== 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>

== 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

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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/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>
+<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]. 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='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='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>
@@ Line 10: / Line 10: @@
 == 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>
+<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/>