Heme Oxygenase Complex Research Articles

Investigation of different substitutions, structure, charge and multiplicity spin of the iron verdoheme-rat heme oxygenase complex: a DFT study

Heme oxygenase-1 (HO-1) is an inducible stress protein that degrades heme to carbon monoxide, iron and biliverdin, which subsequently reduces to bilirubin. Many parameters of verdoheme–rat heme oxygenase complex structure and their role and function on heme degradation were unknown. In this work the structure of iron verdoheme in complex with rat heme oxygenase was studied by density functional theory based B3LYP method and 6-31G basis set. The main goal is to obtain structural and energetic information for various transition states and intermediates on reaction pathways. The charge of verdoheme and iron as the central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effect on the verdoheme ring stabilization and their arrangement are discussed. Gas phase computation has shown that the central metal of the five coordinated rat-verdohemeas ferrous (Fe[Formula: see text] (from 1a-1i) and ferric (Fe[Formula: see text] (from 1j–1q). The Mulliken and NBO charge and spin calculation show that iron is considered as ferrous in all of the optimized structures. Assessment results can gain valuable chemical insight into the electronic reorganization during the reactions.

Multiplicity spin, structure, and charge of iron-verdohemeoxygenase complex: A comparison study by the DFT method

Recently the three-dimensional structure of verdoheme heme oxygenase complex was revealed. However, many parameters of verdoheme heme oxygenase’s complex structure and their role and function on Heme degradation were unknown. In this work the structure of iron verdoheme in complex with heme oxygenase was compared by the density functional theory (DFT)-based B3LYP method using the 6-31G basis set. Many parameters such as charge of verdoheme and iron as central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effects on verdoheme ring stabilization and their arrangement are discussed and compared for twelve different conformations of the molecules to find the most energetically stable states.

A microfluidic-based protein crystallization method in 10 micrometer-sized crystallization space

Protein crystallization and subsequent X-ray diffraction analysis of the three-dimensional structure are necessary for elucidation of the biological functions of proteins and effective rational drug design. Therefore, controlling protein crystallization is important to obtain high resolution X-ray diffraction data. Here, a simple microfluidic method using chips with 10 and 50 μm high crystallization chambers to selectively form suitable single protein crystals for X-ray analysis is demonstrated. As proof of concept, three different types of proteins: lysozyme, glucokinase from Pseudoalteromonas sp. AS-131 (PsGK), and NADPH-cytochrome P450 oxidoreductase–heme oxygenase complex were crystallized. We demonstrate that the crystal growth orientation depends on the height of the crystallization chamber regardless of the protein type. Our results suggest that the confined micro space induces the protein molecules to adhere to a specific crystal face and affects the growth kinetics of each crystal face. The present microfluidic-based protein crystallization method can reform a suitable single protein crystal for X-ray analysis from aggregates of needle-shaped protein crystals.

Crystallographic studies of heme oxygenase complexed with an unstable reaction intermediate, verdoheme

This article discusses the accuracy of X-ray structural studies of heme oxygenase (HO) in complex with an unstable intermediate, verdoheme. Heme degradation by HO proceeds through three successive steps of O2 activation. The mechanism of the third step, the ring opening of verdoheme, has been the least understood. Recent structural studies of the verdoheme–HO complex provide detailed information concerning this mechanism. Due to X-ray-induced photoreduction and the instability of verdoheme, it has been difficult to obtain an accurate structure for the ferrous verdoheme–HO complex. Therefore, accurate structural studies, including analysis of the electronic state of the verdoheme–HO complex, are needed to elucidate the proper reaction mechanism.

Heme Oxygenase Reveals Its Strategy for Catalyzing Three Successive Oxygenation Reactions

Heme oxygenase (HO) is an enzyme that catalyzes the regiospecific conversion of heme to biliverdin IXalpha, CO, and free iron. In mammals, HO has a variety of physiological functions, including heme catabolism, iron homeostasis, antioxidant defense, cellular signaling, and O(2) sensing. The enzyme is also found in plants (producing light-harvesting pigments) and in some pathogenic bacteria, where it acquires iron from the host heme. The HO-catalyzed heme conversion proceeds through three successive oxygenations, a process that has attracted considerable attention because of its reaction mechanism and physiological importance. The HO reaction is unique in that all three O(2) activations are affected by the substrate itself. The first step is the regiospecific self-hydroxylation of the porphyrin alpha-meso carbon atom. The resulting alpha-meso-hydroxyheme reacts in the second step with another O(2) to yield verdoheme and CO. The third O(2) activation, by verdoheme, cleaves its porphyrin macrocycle to release biliverdin and free ferrous iron. In this Account, we provide an overview of our current understanding of the structural and biochemical properties of the complex self-oxidation reactions in HO catalysis. The first meso-hydroxylation is of particular interest because of its distinct contrast with O(2) activation by cytochrome P450. Although most heme enzymes oxidize exogenous substrates by high-valent oxo intermediates, HO was proposed to utilize the Fe-OOH intermediate for the self-hydroxylation. We have succeeded in preparing and characterizing the Fe-OOH species of HO at low temperature, and an analysis of its reaction, together with mutational and crystallographic studies, reveals that protonation of Fe-OOH by a distal water molecule is critical in promoting the unique self-hydroxylation. The second oxygenation is a rapid, spontaneous auto-oxidation of the reactive alpha-meso-hydroxyheme; its mechanism remains elusive, but the HO enzyme has been shown not to play a critical role in it. Until recently, the means of the third O(2) activation had remained unclear as well, but we have recently untangled its mechanistic outline. Reaction analysis of the verdoheme-HO complex strongly suggests the Fe-OOH species as a key intermediate of the ring-opening reaction. This mechanism is very similar to that of the first meso-hydroxylation, including the critical roles of the distal water molecule. A comprehensive study of the three oxygenations of HO highlights the rational design of the enzyme architecture and its catalytic mechanism. Elucidation of the last oxygenation step has enabled a kinetic analysis of the rate-determining step, making it possible to discuss the HO reaction mechanism in relation to its physiological functions.

The Ferrous Verdoheme−Heme Oxygenase Complex is Six-Coordinate and Low-Spin

A biosynthetic and enzymatic method was developed for the preparation of 13C-labeled verdoheme, which permits the 13C NMR spectroscopic characterization of this elusive intermediate in the heme oxidation path catalyzed by the enzyme heme oxygenase. The 13C NMR data indicate that the ferrous verdoheme complex of Neisseria meningitides heme oxygenase is hexacoordinate and diamagnetic, with a proximal histidine and likely a distal hydroxide as axial ligands. The coordination number and spin state of the ferrous verdoheme-heme oxygenase complex is in stark contrast to the pentacoordinate and paramagnetic nature of the heme-heme oxygenase complex and heme centers in general.

Crystal structures of ferrous and CO-, CN(-)-, and NO-bound forms of rat heme oxygenase-1 (HO-1) in complex with heme: structural implications for discrimination between CO and O2 in HO-1.

Heme oxygenase (HO) catalyzes heme degradation by utilizing O(2) and reducing equivalents to produce biliverdin IX alpha, iron, and CO. To avoid product inhibition, the heme[bond]HO complex (heme[bond]HO) is structured to markedly increase its affinity for O(2) while suppressing its affinity for CO. We determined the crystal structures of rat ferrous heme[bond]HO and heme[bond]HO bound to CO, CN(-), and NO at 2.3, 1.8, 2.0, and 1.7 A resolution, respectively. The heme pocket of ferrous heme-HO has the same conformation as that of the previously determined ferric form, but no ligand is visible on the distal side of the ferrous heme. Fe[bond]CO and Fe[bond]CN(-) are tilted, whereas the Fe[bond]NO is bent. The structure of heme[bond]HO bound to NO is identical to that bound to N(3)(-), which is also bent as in the case of O(2). Notably, in the CO- and CN(-)-bound forms, the heme and its ligands shift toward the alpha-meso carbon, and the distal F-helix shifts in the opposite direction. These shifts allow CO or CN(-) to bind in a tilted fashion without a collision between the distal ligand and Gly139 O and cause disruption of one salt bridge between the heme and basic residue. The structural identity of the ferrous and ferric states of heme[bond]HO indicates that these shifts are not produced on reduction of heme iron. Neither such conformational changes nor a heme shift occurs on NO or N(3)(-) binding. Heme[bond]HO therefore recognizes CO and O(2) by their binding geometries. The marked reduction in the ratio of affinities of CO to O(2) for heme[bond]HO achieved by an increase in O(2) affinity [Migita, C. T., Matera, K. M., Ikeda-Saito, M., Olson, J. S., Fujii, H., Yoshimura, T., Zhou, H., and Yoshida, T. (1998) J. Biol. Chem. 273, 945-949] is explained by hydrogen bonding and polar interactions that are favorable for O(2) binding, as well as by characteristic structural changes in the CO-bound form.

Solution 1H NMR Investigation of the Active Site Molecular and Electronic Structures of Substrate-bound, Cyanide-inhibited HmuO, a Bacterial Heme Oxygenase fromCorynebacterium diphtheriae

The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.

Solution NMR Characterization of an Unusual Distal H-bond Network in the Active Site of the Cyanide-inhibited, Human Heme Oxygenase Complex of the Symmetric Substrate, 2,4-Dimethyldeuterohemin

The presence of variable static hemin orientational disorder about the alpha-gamma-meso axis in the substrate complexes of mammalian heme oxygenase, together with the incomplete averaging of a second, dynamic disorder, for each hemin orientation, has led to NMR spectra with severe spectral overlap and loss of key two-dimensional correlations that seriously interfere with structural characterization in solution. We demonstrate that the symmetric substrate, 2,4-dimethyldeuterohemin, yields a single solution species for which the dynamic disorder is sufficiently rapid to allow effective and informative (1)H NMR structural characterization. A much more extensive, effective, and definitive NMR characterization of the cyanide-inhibited, symmetric heme complex of human heme oxygenase shows that the active site structure, with some minor differences, is essentially the same as that for the native protohemin in solution and crystal. A unique distal network that involves particularly strong hydrogen bonds, as well as inter-aromatic contacts, is described that is proposed to stabilize the position of the catalytically critical distal helix Asp-140 carboxylate (Liu, Y., Koenigs Lightning, L., Huang, H., Moënne-Loccoz, P., Schuller, D. J., Poulos, T. L., Loehr, T. M., and Ortiz de Montellano, P. R. (2000) J. Biol. Chem. 275, 34501-34507). The potential role of this network in placing a water molecule to stabilize the hydroperoxy species and as a template for the condensation of the distal helix upon substrate binding are discussed.

Separation and identification of the regioisomers of verdoheme by reversed-phase ion-pair high-performance liquid chromatography, and characterization of their complexes with heme oxygenase

We report an HPLC method for separating the four regioisomers of verdoheme formed in the coupled oxidation of hemin with oxygen and ascorbate in aqueous pyridine. The reversed-phase ion-pair system uses hexafluoroacetone and pyridine as ion-pair agents. The regiochemistry of the separated isomers was established both by HPLC of the corresponding biliverdin IX derivatives and by 1H NMR of each isomer. Optical spectra of the pyridine verdohemochrome isomers were similar to each other, but showed differences in the absorption maxima in the red region, which appear at 680, 663, 648 and 660 nm for the α, β, γ, and δ-isomers, respectively. Each of the four isomers was incorporated anaerobically into heme oxygenase-1, yielding the corresponding verdoheme–enzyme complex. The ferrous forms had absorption maxima at 690, 667, 655, and 663 nm, and their CO-bound forms had maxima at 638, 624, 616, and 626 nm for α, β, γ, and δ-isomer, respectively. Addition of ferricyanide to the α-verdoheme–heme oxygenase complex brought about a ferric low-spin heme-like signal, which is identical with the ferric α-verdoheme complexed with the heme oxygenase that was observed in the heme oxygenase reaction.

Identification of histidine 25 as the heme ligand in human liver heme oxygenase.

Electronic and resonance Raman spectroscopic studies are reported for the His25Ala mutant of human liver heme oxygenase (HO) and its complex with heme. In the oxidized (ferric) form of the enzyme.substrate complex, the heme is shown to be in a high-spin, five-coordinate state. This is distinct from the same complex in the wild-type enzyme in which the heme is six-coordinate, ligated to a proximal histidine and a water molecule in an environment reminiscent of aquometmyoglobin. The reduced (ferrous) form of the complex of the H25A heme oxygenase mutant has lost the very prominent resonance Raman band at approximately 217 cm-1 seen in the wild-type complex that has been unambiguously assigned to the proximal Fe-N(His) vibrational frequency [Sun et al. (1993) Biochemistry 32, 14151; Takahashi et al. (1994) Biochemistry 33, 1010]. The absence of this band in the spectrum of the mutant protein definitively identifies His 25 as the proximal ligand of the heme substrate. Furthermore, this ferrous heme-H25A HO complex exists as an equilibrium mixture between a five-coordinate, high-spin species and a four-coordinate, intermediate-spin species. Although the H25A mutant protein shows no heme oxygenase activity, the heme is competent to bind carbon monoxide. Studies of the CO adduct of the H25A HO complex show v(CO) and v(Fe-CO) frequencies at 1960 and 529 cm-1, respectively, that are characteristic of a hydrophobic carbon monoxide binding site on a heme with a weak proximal ligand.(ABSTRACT TRUNCATED AT 250 WORDS)

Modification of the heme·heme oxygenase system with iron and cobalt tetrasulfonated phthalocyanines

Modification of heme·heme oxygenase by iron(III) and cobalt(II) tetrasulfonated phthalocyanines has been performed. New compounds have been isolated and their properties have been investigated by difference spectroscopy, electrophoresis, molecular weight estimation, electron paramagnetic resonance (EPR) and carboxymethylation at histidyl groups. Spectrophotometric titration data indicate the ratio of the reagents in this process to be 1:1. The visible absorption spectra show the main peak at 650 nm for the iron compound and 682 nm for the cobalt one. Electrophoresis and molecular weight estimation show both complexes to be monomers. Cobalt(II) tetrasulfonated phthalocyanine, under aerobic conditions with heme oxygenase protein, undergoes autooxidation to the cobalt(III) complex, as has been proved by EPR and spectroscopic data. Iron and cobalt phthalocyanine modified heme·heme oxygenase with excess dithionite is reduced at the phthalocyanine ligand. In the presence of oxygen, the reduction product transforms into oxygenated Fe(III)Lheme oxygenase or Co(III)heme oxygenase, respectively. Reduction of the iron(III) model complex with ascorbic acid under anaerobic conditions leads to degradation of the phthalocyanine moiety, while Co(III)heme oxygenase with ascorbic acid is reduced to Co(II)Lheme oxygenase. As has been shown by carboxymethylation of the heme oxygenase protein at the histidine residues, the predominant binding site of both phthalocyanine complexes is the heme-binding histidyl residue. There is evidence that there is a second binding site with lower affinity towards Co(II)L on the heme oxygenase protein. Iron and cobalt tetrasulfonated phthalocyanines are not able to displace heme from the heme·heme oxygenase complex. In this reaction the iron complex undergoes degradation and the cobalt one gives a hybrid compound with heme·heme oxygenase Heme oxygenase protein complexes with iron and cobalt tetrasulfonated phthalocyanines do not exhibit activity in their oxidative degradation.

Inability of the NADH-cytochrome b5 reductase system to initiate heme degradation yielding biliverdin IXα from the oxygenated form of heme · heme oxygenase complex

FEBS LettersVolume 115, Issue 2 p. 278-280 Full-length articleFree Access Inability of the NADH-cytochrome b 5 reductase system to initiate heme degradation yielding biliverdin IXα from the oxygenated form of heme · heme oxygenase complex Tadashi Yoshida, Tadashi Yoshida Department of Biochemistry, Tohoku University School of Medicine, Sendai 980, JapanSearch for more papers by this authorMasato Noguchi, Masato Noguchi Department of Biochemistry, Tohoku University School of Medicine, Sendai 980, JapanSearch for more papers by this authorGoro Kikuchi, Goro Kikuchi Department of Biochemistry, Tohoku University School of Medicine, Sendai 980, JapanSearch for more papers by this author Tadashi Yoshida, Tadashi Yoshida Department of Biochemistry, Tohoku University School of Medicine, Sendai 980, JapanSearch for more papers by this authorMasato Noguchi, Masato Noguchi Department of Biochemistry, Tohoku University School of Medicine, Sendai 980, JapanSearch for more papers by this authorGoro Kikuchi, Goro Kikuchi Department of Biochemistry, Tohoku University School of Medicine, Sendai 980, JapanSearch for more papers by this author First published: June 30, 1980 https://doi.org/10.1016/0014-5793(80)81186-0Citations: 11AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume115, Issue2June 30, 1980Pages 278-280 ReferencesRelatedInformation

Oxygenated form of heme . heme oxygenase complex and requirement for second electron to initiate heme degradation from the oxygenated complex.

Oxygenated form of heme . heme oxygenase complex and requirement for second electron to initiate heme degradation from the oxygenated complex.

Nucleotide requirements for the bone marrow heme oxygenase system

Rat bone marrow microsomal heme oxygenase activity has been studied and optimal condition for the measurement of this activity are described. The activity of bone marrow heme oxygenase was linear with time and protein concentration as measured under these assay conditions. Bilirubin formation by the heme oxygenase complex system was observed with either a NADPH generating system or with NADH as electron donor. The enzyme activity for heme degradation supported by NADH proceeds at a comparable rate to that observed with NADPH as reducing equivalent. It thus appears that this oxidation reaction must be more complex than simply involving NADPH as the sole election donor as has been previously proposed.

Purification and properties of heme oxygenase from rat liver microsomes.

Heme oxygenase was purified to apparent homogeneity from liver microsomes of rats which had been treated with either cobaltous chloride or hemin to induce heme oxygenase in the liver and the purified preparations from either rats showed an apparent molecular weight of about 200,000 when estimated by gel filtration on a column of Sephadex G-200, and gave a minimum molecular weight of about 32,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The hepatic heme oxygenase could bind heme to form a heme . heme oxygenase complex showing an absorption peak at 405 nm, and the extinction coefficient at 405 nm of the heme . heme oxygenase complex was 140 mM-1 cm-1. The heme bound to the hepatic heme oxygenase protein was easily converted to biliverdin when the complex was incubated with the NADPH-cytochrome c reductase system in air. The hepatic heme oxygenase appears to have characteristics essentially similar to those of the splenic heme oxygenase (Yoshida, T., and Kikuchi, G. (1978) J. Biol. Chem. 253, 4224 and 4230). The heme oxygenase preparation which was purified from the cobalt-treated rats contained a small amount of cobaltic protoporphyrin, indicating that cobalt protoporphyrin was synthesized in these rats.