3MOO

Crystal structure of the HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with azide-bound verdoheme

Summary for 3MOO

• Entry DOI: 10.2210/pdb3moo/pdb
• Related: 1IW0 1IW1 1TWN 1TWR 1V8X 2ZVU
• Related PRD ID: PRD_900003
• Descriptor: Heme oxygenase, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, AZIDE ION, ... (6 entities in total)
• Functional Keywords: heme oxygenase, reaction intermediate, ferrous verdoheme, reaction mechanism, anaerobic chamber, absorption spectra, oxidoreductase
• Biological source: Corynebacterium diphtheriae
• Total number of polymer chains: 2
• Total formula weight: 51308.52

Authors

Omori, K.,Matsui, T.,Unno, M.,Ikeda-Saito, M. (deposition date: 2010-04-22, release date: 2011-03-09, Last modification date: 2023-11-01)

Primary citation

Lai, W.,Chen, H.,Matsui, T.,Omori, K.,Unno, M.,Ikeda-Saito, M.,Shaik, S.
Enzymatic ring-opening mechanism of verdoheme by the heme oxygenase: a combined X-ray crystallography and QM/MM study.
J.Am.Chem.Soc., 132:12960-12970, 2010

PubMed Abstract: The least understood mechanism during heme degradation by the enzyme heme oxygenase (HO) is the third step of ring opening of verdoheme to biliverdin, a process which maintains iron homeostasis. In response to this mechanistic uncertainty, we launched a combined study of X-ray crystallography and theoretical QM/MM calculations, designed to elucidate the mechanism. The air-sensitive ferrous verdoheme complex of HmuO, a heme oxygenase from Corynebacterium diphtheriae, was crystallized under anaerobic conditions. Spectral analysis of the azide-bound verdoheme-HmuO complex crystals assures that the verdoheme group remains intact during the crystallization and X-ray diffraction measurement. The structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. The subsequent QM/MM calculations based on this crystal structure explore the reaction mechanisms starting from the FeOOH-verdoheme and FeHOOH-verdoheme complexes, which mimic, respectively, the O(2)- and H(2)O(2)-supported degradations. In both mechanisms, the rate-determining step is the initial O-O bond breaking step, which is either homolytic (for FeHOOH-verdoheme) or coupled to electron and proton transfers (in FeOOH-verdoheme). Additionally, the calculations indicate that the FeHOOH-verdoheme complex is more reactive than the FeOOH-verdoheme complex in accord with experimental findings. QM energies with embedded MM charges are close to and yield the same conclusions as full QM/MM energies. Finally, the calculations highlight the dominant influence of the distal water cluster which acts as a biocatalyst for the conversion of verdoheme to biliverdin in the two processes, by fixing the departing OH and directing it to the requisite site of attack, and by acting as a proton shuttle and a haven for the highly reactive OH(-) nucleophile.

PubMed: 20806922
DOI: 10.1021/ja104674q

Experimental method

X-RAY DIFFRACTION (1.71 Å)