8OMM

Coproporphyrin III - LmCpfC complex soaked 3min with Fe2+

Summary for 8OMM

• Entry DOI: 10.2210/pdb8omm/pdb
• Descriptor: Coproporphyrin III ferrochelatase, GLYCEROL, 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: ferrochelatase, monomere, heme b, biosynthesis, iron insertion, metal binding protein
• Biological source: Listeria monocytogenes
• Total number of polymer chains: 1
• Total formula weight: 36484.08

Authors

Gabler, T.,Hofbauer, S. (deposition date: 2023-03-31, release date: 2023-05-03, Last modification date: 2023-12-06)

Primary citation

Gabler, T.,Dali, A.,Sebastiani, F.,Furtmuller, P.G.,Becucci, M.,Hofbauer, S.,Smulevich, G.
Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species.
Protein Sci., 32:e4788-e4788, 2023

PubMed Abstract: Understanding the reaction mechanism of enzymes at the molecular level is generally a difficult task, since many parameters affect the turnover. Often, due to high reactivity and formation of transient species or intermediates, detailed information on enzymatic catalysis is obtained by means of model substrates. Whenever possible, it is essential to confirm a reaction mechanism based on substrate analogues or model systems by using the physiological substrates. Here we disclose the ferrous iron incorporation mechanism, in solution, and in crystallo, by the coproporphyrin III-coproporphyrin ferrochelatase complex from the firmicute, pathogen, and antibiotic resistant, Listeria monocytogenes. Coproporphyrin ferrochelatase plays an important physiological role as the metalation represents the penultimate reaction step in the prokaryotic coproporphyrin-dependent heme biosynthetic pathway, yielding coproheme (ferric coproporphyrin III). By following the metal titration with resonance Raman spectroscopy and x-ray crystallography, we prove that upon metalation the saddling distortion becomes predominant both in the crystal and in solution. This is a consequence of the readjustment of hydrogen bond interactions of the propionates with the protein scaffold during the enzymatic catalysis. Once the propionates have established the interactions typical of the coproheme complex, the distortion slowly decreases, to reach the almost planar final product.

PubMed: 37743577
DOI: 10.1002/pro.4788

Experimental method

X-RAY DIFFRACTION (2.15 Å)