Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae

Unno, Masaki; Matsui, Toshitaka; Chu, Grace C.; Couture, Manon; Yoshida, Tadashi; Rousseau, Denis L.; Olson, John S.; Ikeda‐Saito, Masao

doi:10.1074/jbc.m400491200

Cited by 100 publications

(178 citation statements)

References 57 publications

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“…The increased hydrophobicity of the active site upon the exclusion of water would also aid the stabilization of an oxyferrous species. Studies with heme oxygenase suggest that the hydrogen-bonding interactions to the dioxygen substrate may also help to prevent its heterolysis (20), and the exclusion of water probably removes a hydrogen-bond competitor to the dioxygen. After the initial attack by the C3 atom, the reaction may proceed via a Criegee rearrangement or a dioxetane intermediate (SI Fig.…”

Section: Resultsmentioning

confidence: 99%

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Forouhar

Anderson

Mowat

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

169

284

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Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive structural and biochemical studies of the Xanthomonas campestris TDO and a related protein SO4414 from Shewanella oneidensis, including the structure at 1.6-Å resolution of the catalytically active, ferrous form of TDO in a binary complex with the substrate L-Trp. The carboxylate and ammonium moieties of tryptophan are recognized by electrostatic and hydrogen-bonding interactions with the enzyme and a propionate group of the heme, thus defining the L-stereospecificity. A second, possibly allosteric, L-Trp-binding site is present at the tetramer interface. The sixth coordination site of the heme-iron is vacant, providing a dioxygenbinding site that would also involve interactions with the ammonium moiety of L-Trp and the amide nitrogen of a glycine residue. The indole ring is positioned correctly for oxygenation at the C2 and C3 atoms. The active site is fully formed only in the binary complex, and biochemical experiments confirm this induced-fit behavior of the enzyme. The active site is completely devoid of water during catalysis, which is supported by our electrochemical studies showing significant stabilization of the enzyme upon substrate binding.cancer ͉ heme enzymes ͉ immunomodulation ͉ indoleamine 2,3-dioxygenase T ryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) catalyze the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring, the first and rate-limiting step in L-Trp catabolism through the kynurenine pathway (1-3). In addition, IDO has been implicated in a diverse range of physiological and pathological conditions, including suppression of T cell proliferation, maternal tolerance to allogenic fetus, and immune escape of cancers (4-8), and is an attractive target for drug discovery against cancer and autoimmune and other diseases (2, 9-12).Despite catalyzing identical biochemical reactions (Fig. 1a), the sequence similarity between TDO and IDO is extremely low. An alignment of their sequences is only possible based on their structures, which suggests a sequence identity of 10% between them (Fig. 1b). In comparison, Xanthomonas campestris TDO shares 34% sequence identity with human TDO (Fig. 1b), demonstrating the remarkable evolutionary conservation of this enzyme. TDO is a homotetrameric enzyme and is highly specific for L-Trp and related derivatives such as 6-fluoro-Trp as the substrate. In comparison, IDO is monomeric, and shows activity toward a larger collection of substrates, including L-Trp, Dtryptophan (D-Trp), serotonin, and tryptamine (3), although the K m for D-Trp is Ϸ100-fold higher than that for L-Trp (13). The structure of human IDO in the catalytically inactive, ferric [Fe(III)]-heme state in complex with the 4-phenylimidazole inhibitor has recently been reported (14). Although this structure gave information about important active site residues, the inhibitor is coordinat...

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Section: Resultsmentioning

confidence: 99%

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Forouhar

Anderson

Mowat

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

169

284

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“…However, we failed to confirm this, and rather found that these two residues affected neither the binding to CPR nor the NADPH-CPR-supported HO activity. Yoshida's group also showed that replacement of Lys 18 and Lys 22 with Ala did not affect the reduction rate of the heme bound to HO-1 (66). As described above, our docking model shows a close contact between Lys 149 in the distal F helix of HO-1 and the acidic clusters near the FMN site of CPR (Fig.…”

Section: Single Turnover Reactions Of Heme Complexes Of Ho-1 Mutants-mentioning

confidence: 99%

“…The FMN domain of CPR is of particular importance for interaction with redox partners, because FMN acts as the exit point of electrons to heme. Interestingly, the FRET study showed that Lys 18 and Lys 22 in the proximal A helix of HO-1 are involved in the interaction with CPR (50). However, we failed to confirm this, and rather found that these two residues affected neither the binding to CPR nor the NADPH-CPR-supported HO activity.…”

Section: Single Turnover Reactions Of Heme Complexes Of Ho-1 Mutants-mentioning

confidence: 99%

Involvement of NADP(H) in the Interaction between Heme Oxygenase-1 and Cytochrome P450 Reductase

Higashimoto

Sakamoto

Hayashi

et al. 2005

Journal of Biological Chemistry

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“…Dioxygen-bound cdHO has two strong hydrogen bonds that can preferentially stabilize the highly polar Fe⅐O 2 complex (29). One interaction is with the amide NH of Gly-139, and the other is with the distal pocket water molecule.…”

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confidence: 99%

“…The greater polarity of the bound O 2 ligand also plays a role in enhancing the affinity of O 2 relative to CO for both the globins and HO enzymes. The partition constant (M), defined as the ratio of the equilibrium association constants for CO and O 2 (K CO /K O2 ), is ϳ30,000 for free heme, whereas that for sperm whale myoglobin is only ϳ40 and is further reduced to ϳ4 for human heme oxygenase (28,29). The O 2 affinities of mammalian HO-1 and HO-2 are 30 -90-fold higher than those of mammalian myoglobins (28), whereas the O 2 affinity of the bacterial HO from C. diphtheriae is 20-fold higher than that of myoglobin (29).…”

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confidence: 99%

Diatomic Ligand Discrimination by the Heme Oxygenases from Neisseria meningitidis and Pseudomonas aeruginosa

Friedman

Meharenna

Wilks

et al. 2007

Journal of Biological Chemistry

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Heme oxygenases have an increased binding affinity for O 2 relative to CO. Such discrimination is critical to the function of HO enzymes because one of the main products of heme catabolism is CO. Kinetic studies of mammalian and bacterial HO proteins reveal a significant decrease in the dissociation rate of O 2 relative to other heme proteins such as myoglobin. Here we report the kinetic rate constants for the binding of O 2 and CO by the heme oxygenases from Neisseria meningitidis (nmHO) and Pseudomonas aeruginosa (paHO). A combination of stoppedflow kinetic and laser flash photolysis experiments reveal that nmHO and paHO both maintain a similar degree of ligand discrimination as mammalian HO-1 and the HO from Corynebacterium diphtheriae. However, in addition to the observed decrease in dissociation rate for O 2 by both nmHO and paHO, kinetic analyses show an increase in dissociation rate for CO by these two enzymes. The crystal structures of nmHO and paHO both contain significant differences from the mammalian HO-1 and bacterial C. diphtheriae HO structures, which suggests a structural basis for ligand discrimination in nmHO and paHO. Heme oxygenase (HO)2 catalyzes the oxidative degradation of heme to biliverdin, iron, and CO (Fig. 1). HO has been identified in a wide array of organisms, including mammals (1, 2), insects (3, 4), and photosynthetic organisms (5, 6). Of particular interest, HO is present in many pathogenic bacteria (7-10), including Neisseria meningitidis (11) and Pseudomonas aeruginosa (12). These pathogenic bacteria have developed sophisticated heme uptake systems that harness the iron from hemecontaining proteins present in the host (13-15). The HO enzymes from N. meningitidis (nmHO) and P. aeruginosa (paHO) are both essential for the utilization of iron from imported heme, and the crystal structures of these two bacterial HO enzymes have now been solved (16,17). Although most HOs hydroxylate exclusively the ␣-meso heme carbon (Fig. 1), paHO is unusual because the ␥-meso carbon is the predominate site of hydroxylation (18) even though the structure paHO is very much the same as other HOs. The difference in hydroxylation patterns is due to an ϳ100 o rotation of the heme in paHO relative to other HOs which places the ␥-meso carbon at the same position in the active site as the ␣-meso carbon in other HOs (16).The Fe(II) atom of the heme prosthetic group of heme proteins is an efficient binder of O 2 , NO, and CO, and the binding by heme proteins of these diatomic molecules is of critical importance to physiological processes such as respiration, vasodilation, and neurotransmission (19 -21). A common feature shared by all heme proteins is the need to not only bind its target ligand but also to discriminate against the binding of heme ligands of similar size and shape. Fe(II) adducts of CO are normally linear because backbonding is optimized by the overlap of Fe(II) d-orbitals with the empty * orbitals of . In contrast, Fe(II)-NO and Fe(II)-O 2 are naturally bent in order to maximize overlap with ...

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Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae

Cited by 100 publications

References 57 publications

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Involvement of NADP(H) in the Interaction between Heme Oxygenase-1 and Cytochrome P450 Reductase

Diatomic Ligand Discrimination by the Heme Oxygenases from Neisseria meningitidis and Pseudomonas aeruginosa

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