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| | <StructureSection load='6xub' size='340' side='right'caption='[[6xub]], [[Resolution|resolution]] 1.78Å' scene=''> | | <StructureSection load='6xub' size='340' side='right'caption='[[6xub]], [[Resolution|resolution]] 1.78Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6xub]] 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=6XUB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XUB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6xub]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XUB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VOV:harderoheme+(III)'>VOV</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]] 1.78Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VOV:harderoheme+(III)'>VOV</scene></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=6xub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xub OCA], [http://pdbe.org/6xub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xub RCSB], [http://www.ebi.ac.uk/pdbsum/6xub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xub 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=6xub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xub OCA], [https://pdbe.org/6xub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xub RCSB], [https://www.ebi.ac.uk/pdbsum/6xub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xub ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q6NGV6_CORDI Q6NGV6_CORDI] Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate intermediate.[HAMAP-Rule:MF_02244] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus diphtheriae kruse in flugge 1886]] | + | [[Category: Corynebacterium diphtheriae]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Djinovic-Carugo, K]] | + | [[Category: Djinovic-Carugo K]] |
| - | [[Category: Furtmueller, P G]] | + | [[Category: Furtmueller PG]] |
| - | [[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: Actinobacterial]]
| + | |
| - | [[Category: Coproheme decarboxylase]]
| + | |
| - | [[Category: Decarboxylation]]
| + | |
| - | [[Category: Ferredoxin like]]
| + | |
| - | [[Category: Heme b biosynthesis]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
Q6NGV6_CORDI Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate intermediate.[HAMAP-Rule:MF_02244]
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Michlits H, Lier B, Pfanzagl V, Djinovic-Carugo K, Furtmuller PG, Oostenbrink C, Obinger C, Hofbauer S. Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation. ACS Catal. 2020 May 15;10(10):5405-5418. doi: 10.1021/acscatal.0c00411. Epub 2020, Apr 9. PMID:32440366 doi:http://dx.doi.org/10.1021/acscatal.0c00411
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