Crystal structure of the dioxygen-bound heme oxygenase from Corynebacterium diphtheriae: implications for heme oxygenase function. 2004

Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan. unno19@tagen.tohoku.ac.jp

HmuO, a heme oxygenase of Corynebacterium diphtheriae, catalyzes degradation of heme using the same mechanism as the mammalian enzyme. The oxy form of HmuO, the precursor of the catalytically active ferric hydroperoxo species, has been characterized by ligand binding kinetics, resonance Raman spectroscopy, and x-ray crystallography. The oxygen association and dissociation rate constants are 5 microm(-1) s(-1) and 0.22 s(-1), respectively, yielding an O(2) affinity of 21 microm(-1), which is approximately 20 times greater than that of mammalian myoglobins. However, the affinity of HmuO for CO is only 3-4-fold greater than that for mammalian myoglobins, implying the presence of strong hydrogen bonding interactions in the distal pocket of HmuO that preferentially favor O(2) binding. Resonance Raman spectra show that the Fe-O(2) vibrations are tightly coupled to porphyrin vibrations, indicating the highly bent Fe-O-O geometry that is characteristic of the oxy forms of heme oxygenases. In the crystal structure of the oxy form the Fe-O-O angle is 110 degrees, the O-O bond is pointed toward the heme alpha-meso-carbon by direct steric interactions with Gly-135 and Gly-139, and hydrogen bonds occur between the bound O(2) and the amide nitrogen of Gly-139 and a distal pocket water molecule, which is a part of an extended hydrogen bonding network that provides the solvent protons required for oxygen activation. In addition, the O-O bond is orthogonal to the plane of the proximal imidazole side chain, which facilitates hydroxylation of the porphyrin alpha-meso-carbon by preventing premature O-O bond cleavage.

UI MeSH Term Description Entries
D008322 Mammals Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young. Mammalia,Mammal
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009211 Myoglobin A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.
D010100 Oxygen An element with atomic symbol O, atomic number 8, and atomic weight [15.99903; 15.99977]. It is the most abundant element on earth and essential for respiration. Dioxygen,Oxygen-16,Oxygen 16
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D003353 Corynebacterium diphtheriae A species of gram-positive, asporogenous bacteria in which three cultural types are recognized. These types (gravis, intermedius, and mitis) were originally given in accordance with the clinical severity of the cases from which the different strains were most frequently isolated. This species is the causative agent of DIPHTHERIA.
D006419 Heme Oxygenase (Decyclizing) A mixed function oxidase enzyme which during hemoglobin catabolism catalyzes the degradation of heme to ferrous iron, carbon monoxide and biliverdin in the presence of molecular oxygen and reduced NADPH. The enzyme is induced by metals, particularly cobalt. Haem Oxygenase,Heme Oxygenase,Oxygenase, Haem,Oxygenase, Heme
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D013059 Spectrum Analysis, Raman Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light. Raman Spectroscopy,Analysis, Raman Spectrum,Raman Optical Activity Spectroscopy,Raman Scattering,Raman Spectrum Analysis,Scattering, Raman,Spectroscopy, Raman

Related Publications

Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
July 1999, The Journal of biological chemistry,
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
March 2004, The Journal of biological chemistry,
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
June 2000, The Journal of biological chemistry,
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
November 2015, Biochemistry,
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
September 2003, The Journal of biological chemistry,
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
August 2015, Molecules and cells,
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
January 1952, Biokhimiia (Moscow, Russia),
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
January 1957, Biokhimiia (Moscow, Russia),
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
November 2013, The Journal of biological chemistry,
Masaki Unno, and Toshitaka Matsui, and Grace C Chu, and Manon Couture, and Tadashi Yoshida, and Denis L Rousseau, and John S Olson, and Masao Ikeda-Saito
January 1998, The Journal of biological chemistry,
Copied contents to your clipboard!