5LOQ

Structure of coproheme bound HemQ from Listeria monocytogenes

Summary for 5LOQ

• Entry DOI: 10.2210/pdb5loq/pdb
• Descriptor: Putative heme-dependent peroxidase lmo2113, SODIUM ION, 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX, ... (5 entities in total)
• Functional Keywords: hemq, heme biosynthesis, coproheme, heme b, gram-positive pathogens, oxidoreductase
• Biological source: Listeria monocytogenes
• Total number of polymer chains: 5
• Total formula weight: 147887.97

Authors

Puehringer, D.,Mlynek, G.,Hofbauer, S.,Djinovic-Carugo, K.,Obinger, C. (deposition date: 2016-08-09, release date: 2016-10-26, Last modification date: 2024-01-10)

Primary citation

Hofbauer, S.,Mlynek, G.,Milazzo, L.,Puhringer, D.,Maresch, D.,Schaffner, I.,Furtmuller, P.G.,Smulevich, G.,Djinovic-Carugo, K.,Obinger, C.
Hydrogen peroxide-mediated conversion of coproheme to heme b by HemQ-lessons from the first crystal structure and kinetic studies.
FEBS J., 283:4386-4401, 2016

PubMed Abstract: Heme biosynthesis in Gram-positive bacteria follows a recently described coproporphyrin-dependent pathway with HemQ catalyzing the decarboxylation of coproheme to heme b. Here we present the first crystal structure of a HemQ (homopentameric coproheme-HemQ from Listeria monocytogenes) at 1.69 Å resolution and the conversion of coproheme to heme b followed by UV-vis and resonance Raman spectroscopy as well as mass spectrometry. The ferric five-coordinated coproheme iron of HemQ is weakly bound by a neutral proximal histidine H174. In the crystal structure of the resting state, the distal Q187 (conserved in Firmicutes HemQ) is H-bonded with propionate p2 and the hydrophobic distal cavity lacks solvent water molecules. Two H O molecules are shown to be necessary for decarboxylation of the propionates p2 and p4, thereby forming the corresponding vinyl groups of heme b. The overall reaction is relatively slow (k /K = 1.8 × 10 m ·s at pH 7.0) and occurs in a stepwise manner with a three-propionate intermediate. We present the noncovalent interactions between coproheme and the protein and propose a two-step reaction mechanism. Furthermore, the structure of coproheme-HemQ is compared to that of the phylogenetically related heme b-containing chlorite dismutases.

PubMed: 27758026
DOI: 10.1111/febs.13930

Experimental method

X-RAY DIFFRACTION (1.69 Å)