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==Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with coproheme== | ==Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with coproheme== | ||
<StructureSection load='6xuc' size='340' side='right'caption='[[6xuc]]' scene=''> | <StructureSection load='6xuc' size='340' side='right'caption='[[6xuc]], [[Resolution|resolution]] 1.87Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XUC FirstGlance]. <br> | <table><tr><td colspan='2'>[[6xuc]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_diphtheriae"_kruse_in_flugge_1886 "bacillus diphtheriae" kruse in flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XUC FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6xuc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xuc OCA], [http://pdbe.org/6xuc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xuc RCSB], [http://www.ebi.ac.uk/pdbsum/6xuc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xuc ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEC:1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC+ACID+FERROUS+COMPLEX'>FEC</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">B11Q_01470, BT093_04375 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1717 "Bacillus diphtheriae" Kruse in Flugge 1886])</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6xuc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xuc OCA], [http://pdbe.org/6xuc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xuc RCSB], [http://www.ebi.ac.uk/pdbsum/6xuc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xuc ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Coproheme decarboxylases (ChdCs) catalyze the final step in heme b biosynthesis of monoderm and some diderm bacteria. In this reaction, coproheme is converted to heme b via monovinyl monopropionate deuteroheme (MMD) in two consecutive decarboxylation steps. In Firmicutes decarboxylation of propionates 2 and 4 of coproheme depend on hydrogen peroxide and the presence of a catalytic tyrosine. Here we demonstrate that ChdCs from Actinobacteria are unique in using a histidine (H118 in ChdC from Corynebacterium diphtheriae, CdChdC) as a distal base in addition to the redox-active tyrosine (Y135). We present the X-ray crystal structures of coproheme-CdChdC and MMD-CdChdC, which clearly show (i) differences in the active site architecture between Firmicutes and Actinobacteria and (ii) rotation of the redox-active reaction intermediate (MMD) after formation of the vinyl group at position 2. Distal H118 is shown to catalyze the heterolytic cleavage of hydrogen peroxide (k app = (4.90 +/- 1.25) x 10(4) M(-1) s(-1)). The resulting Compound I is rapidly converted to a catalytically active Compound I* (oxoiron(IV) Y135(*)) that initiates the radical decarboxylation reactions. As a consequence of the more efficient Compound I formation, actinobacterial ChdCs exhibit a higher catalytic efficiency in comparison to representatives from Firmicutes. On the basis of the kinetic data of wild-type CdChdC and the variants H118A, Y135A, and H118A/Y135A together with high-resolution crystal structures and molecular dynamics simulations, we present a molecular mechanism for the hydrogen peroxide dependent conversion of coproheme via MMD to heme b and discuss differences between ChdCs from Actinobacteria and Firmicutes. | |||
Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation.,Michlits H, Lier B, Pfanzagl V, Djinovic-Carugo K, Furtmuller PG, Oostenbrink C, Obinger C, Hofbauer S ACS Catal. 2020 May 15;10(10):5405-5418. doi: 10.1021/acscatal.0c00411. Epub 2020, Apr 9. PMID:32440366<ref>PMID:32440366</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6xuc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus diphtheriae kruse in flugge 1886]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Djinovic-Carugo K]] | [[Category: Djinovic-Carugo, K]] | ||
[[Category: Furtmueller | [[Category: Furtmueller, P G]] | ||
[[Category: Hofbauer S]] | [[Category: Hofbauer, S]] | ||
[[Category: Lier B]] | [[Category: Lier, B]] | ||
[[Category: Michlits H]] | [[Category: Michlits, H]] | ||
[[Category: Obinger C]] | [[Category: Obinger, C]] | ||
[[Category: Oostenbrink C]] | [[Category: Oostenbrink, C]] | ||
[[Category: Pfanzagl V]] | [[Category: Pfanzagl, V]] | ||
[[Category: Oxidoreductase]] | |||
Revision as of 09:51, 10 June 2020
Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with coprohemeStructure of coproheme decarboxylase from Corynebacterium diphteriae in complex with coproheme
Structural highlights
Publication Abstract from PubMedCoproheme decarboxylases (ChdCs) catalyze the final step in heme b biosynthesis of monoderm and some diderm bacteria. In this reaction, coproheme is converted to heme b via monovinyl monopropionate deuteroheme (MMD) in two consecutive decarboxylation steps. In Firmicutes decarboxylation of propionates 2 and 4 of coproheme depend on hydrogen peroxide and the presence of a catalytic tyrosine. Here we demonstrate that ChdCs from Actinobacteria are unique in using a histidine (H118 in ChdC from Corynebacterium diphtheriae, CdChdC) as a distal base in addition to the redox-active tyrosine (Y135). We present the X-ray crystal structures of coproheme-CdChdC and MMD-CdChdC, which clearly show (i) differences in the active site architecture between Firmicutes and Actinobacteria and (ii) rotation of the redox-active reaction intermediate (MMD) after formation of the vinyl group at position 2. Distal H118 is shown to catalyze the heterolytic cleavage of hydrogen peroxide (k app = (4.90 +/- 1.25) x 10(4) M(-1) s(-1)). The resulting Compound I is rapidly converted to a catalytically active Compound I* (oxoiron(IV) Y135(*)) that initiates the radical decarboxylation reactions. As a consequence of the more efficient Compound I formation, actinobacterial ChdCs exhibit a higher catalytic efficiency in comparison to representatives from Firmicutes. On the basis of the kinetic data of wild-type CdChdC and the variants H118A, Y135A, and H118A/Y135A together with high-resolution crystal structures and molecular dynamics simulations, we present a molecular mechanism for the hydrogen peroxide dependent conversion of coproheme via MMD to heme b and discuss differences between ChdCs from Actinobacteria and Firmicutes. Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation.,Michlits H, Lier B, Pfanzagl V, Djinovic-Carugo K, Furtmuller PG, Oostenbrink C, Obinger C, Hofbauer S ACS Catal. 2020 May 15;10(10):5405-5418. doi: 10.1021/acscatal.0c00411. Epub 2020, Apr 9. PMID:32440366[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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