6XUC

Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with coproheme

Summary for 6XUC

• Entry DOI: 10.2210/pdb6xuc/pdb
• Descriptor: Chlorite dismutase, 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX (3 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: Corynebacterium diphtheriae
• Total number of polymer chains: 5
• Total formula weight: 139987.49

Authors

Michlits, H.,Lier, B.,Pfanzagl, V.,Djinovic-Carugo, K.,Furtmueller, P.G.,Oostenbrink, C.,Obinger, C.,Hofbauer, S. (deposition date: 2020-01-17, release date: 2020-04-22, Last modification date: 2024-01-24)

Primary citation

Michlits, H.,Lier, B.,Pfanzagl, V.,Djinovic-Carugo, K.,Furtmuller, P.G.,Oostenbrink, C.,Obinger, C.,Hofbauer, S.
Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation.
Acs Catalysis, 10:5405-5418, 2020

PubMed Abstract: Coproheme decarboxylases (ChdCs) catalyze the final step in heme biosynthesis of monoderm and some diderm bacteria. In this reaction, coproheme is converted to heme 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 , ChdC) as a distal base in addition to the redox-active tyrosine (Y135). We present the X-ray crystal structures of coproheme-ChdC and MMD-ChdC, 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 ( = (4.90 ± 1.25) × 10 M s). 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 ChdC 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 and discuss differences between ChdCs from Actinobacteria and Firmicutes.

PubMed: 32440366
DOI: 10.1021/acscatal.0c00411

Experimental method

X-RAY DIFFRACTION (1.8702 Å)