6xuc: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 6xuc is ON HOLD
+==Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with coproheme==
+<StructureSection load='6xuc' size='340' side='right'caption='[[6xuc]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6xuc]] 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=6XUC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XUC 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]] 1.8702&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6xuc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xuc OCA], [https://pdbe.org/6xuc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xuc RCSB], [https://www.ebi.ac.uk/pdbsum/6xuc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xuc ProSAT]</span></td></tr>
+</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;">
+== 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.
-Authors:
+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>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6xuc" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Corynebacterium diphtheriae]]
+[[Category: Large Structures]]
+[[Category: Djinovic-Carugo K]]
+[[Category: Furtmueller PG]]
+[[Category: Hofbauer S]]
+[[Category: Lier B]]
+[[Category: Michlits H]]
+[[Category: Obinger C]]
+[[Category: Oostenbrink C]]
+[[Category: Pfanzagl V]]