Paper Citing NAMD - Abstract
Unno, Masaki; Ardevol, Albert; Rovira, Carme; Ikeda-Saito, Masao
Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae X-RAY CRYSTALLOGRAPHY AND MOLECULAR DYNAMICS INVESTIGATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:34443-34458, NOV 29 2013
Background: Heme oxygenase (HO) converts heme to biliverdin, carbon monoxide, and Fe2+. Results: HO crystal structures were determined for substrate-free Fe3+-biliverdin and biliverdin forms, as well as intermediates of the last two. Conclusion: HO reaction center is built with substrate-induced conformational changes, and Fe2+ is released without major structural changes. Significance: Elucidation of these HO structures is fundamental for understanding its enzyme mechanism. Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe3+-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe3+-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe3+-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe3+-biliverdin and biliverdin complexes has been determined at 1.70 resolution, implying a possible route for iron exit.
