Dehaloperoxidase-hemoglobin from Amphitrite ornata is primarily a monomer in solution

Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B

Dehalperoxidase (DHP) has diverse catalytic activities depending on the substrate binding conformation, pH, and dynamics in the distal pocket above the heme. According to our hypothesis, the molecular structure of the substrate and binding orientation in DHP guide enzymatic function. Enzyme kinetic studies have shown that the catalytic activity of DHP B is significantly higher than that of DHP A despite 96% sequence homology. There are more than 30 substrate-bound structures with DHP B, each providing insight into the nature of enzymatic binding at the active site. By contrast, the only X-ray crystallographic structures of small molecules in a complex with DHP A are phenols. This study is focused on investigating substrate binding in DHP A to compare with DHP B structures. Fifteen substrates were selected that were known to bind to DHP B in the crystal to test whether soaking substrates into DHP A would yield similar structures. Five of these substrates yielded X-ray crystal structures of substrate-bound DHP A, namely, 2,4-dichlorophenol (1.48 Å, PDB: 8EJN), 2,4-dibromophenol (1.52 Å, PDB: 8VSK), 4-nitrophenol (2.03 Å, PDB: 8VKC), 4-nitrocatechol (1.40 Å, PDB: 8VKD), and 4-bromo-o-cresol (1.64 Å, PDB: 8VZR). For the remaining substrates that bind to DHP B, such as cresols, 5-bromoindole, benzimidazole, 4,4-biphenol, 4.4-ethylidenebisphenol, 2,4-dimethoxyphenol, and guaiacol, the electron density maps in DHP A are not sufficient to determine the presence of the substrates, much less their orientation. In our hands, only phenols, 4-Br-o-cresol, and 4-nitrocatechol can be soaked into crystalline DHP A. None of the larger substrates were observed to bind. A minimum of seven hanging drops were selected for soaking with more than 50 crystals screened for each substrate. The five high-quality examples of direct comparison of modes of binding in DHP A and B for the same substrate provide further support for the hypothesis that the substrate-binding conformation determines the enzyme function of DHP.

Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes

Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.

The divergent pH dependence of substrate turnover in dehaloperoxidases A and B

The pH-dependent peroxidase activity in both dehaloperoxidases A and B was studied by a kinetic assay, stopped flow spectroscopy, resonance Raman spectroscopy, and high-performance liquid chromatography at pH 5.0, 6.0, and 7.0. At pH 7.0, both isozymes follow the peroxidase ping-pong kinetic model derived from the three-step reaction scheme using the steady-state approximation. However, deviation from standard saturation behavior is observed at pH < 6.0 and [TCP] > 0.7 mM, owing to multiple processes: a) self-inhibition of TCP by internal binding; b) oxidation of the product by a pH- and concentration-dependent secondary reaction; and c) formation of an inactive species known as compound RH in the absence of oxidizable substrate. Although DHP-A and DHP-B differ by only 5 amino acids, they show a complete trend reversal in their observed peroxidase kinetics and product yields. Although at pH 7.0 DHP-B had higher TCP oxidation activity than DHP-A as reported previously, as pH was lowered, DHP-A appeared to have a higher peroxidase activity than DHP-B. This is an unprecedented result. However, the fact that there are multiple processes contributing to both kinetics and yield of TCP oxidation complicates interpretation of these data. Deactivation via compound RH and self-inhibition are pH dependent reactions that compete with substrate oxidation. Compound RH formation was observed to be rapid at low pH. A complete set of control experiments were conducted to differentiate the various contributions to the observed enzyme kinetics.

SAXS data based global shape analysis of trigger factor (TF) proteins from E. coli, V. cholerae, and P. frigidicola: resolving the debate on the nature of monomeric and dimeric forms

Dimerization of bacterial chaperone trigger factor (TF) is an inherent protein concentration based property which available biophysical characterization and crystal structures have kept debatable. We acquired small-angle X-ray scattering (SAXS) intensity data from different TF homologues from Escherichia coli (ECTF), Vibrio cholerae (VCTF), and Psychrobacter frigidicola (PFTF) while varying each protein concentration. We found that ECTF and VCTF adopt a compact dimeric shape at higher concentrations which did not resemble the "back-to-back" conformation reported earlier for ECTF from crystallography (PDB ID: 1W26 ). In contrast, PFTF remained monomeric throughout the concentration range 2-90 μM displaying a multimodal open extended conformation. OLIGOMER analysis showed that both the ECTF and VCTF remained completely monomeric at lower concentrations (2-11 μM), while, at higher concentrations (60-90 μM), they adopted a dimeric form. Interestingly, the equilibrium existed in the medium concentration range (>11 and <60 μM), which correlates with the physiological concentration (40-50 μM) of TF in cell cytoplasm. Additionally, circular dichroism data revealed that solution structures of ECTF and VCTF contain predominantly α-helical content, while PFTF contains 310-helical content.

Functional consequences of the creation of an Asp-His-Fe triad in a 3/3 globin

The proximal side of dehaloperoxidase-hemoglobin A (DHP A) from Amphitrite ornata has been modified via site-directed mutagenesis of methionine 86 into aspartate (M86D) to introduce an Asp-His-Fe triad charge relay. X-ray crystallographic structure determination of the metcyano forms of M86D [Protein Data Bank (PDB) entry 3MYN ] and M86E (PDB entry 3MYM ) mutants reveal the structural origins of a stable catalytic triad in DHP A. A decrease in the rate of H(2)O(2) activation as well as a lowered reduction potential versus that of the wild-type enzyme was observed in M86D. One possible explanation for the significantly lower activity is an increased affinity for the distal histidine in binding to the heme Fe to form a bis-histidine adduct. Resonance Raman spectroscopy demonstrates a pH-dependent ligation by the distal histidine in M86D, which is indicative of an increased trans effect. At pH 5.0, the heme Fe is five-coordinate, and this structure resembles the wild-type DHP A resting state. However, at pH 7.0, the distal histidine appears to form a six-coordinate ferric bis-histidine (hemichrome) adduct. These observations can be explained by the effect of the increased positive charge on the heme Fe on the formation of a six-coordinate low-spin adduct, which inhibits the ligation and activation of H(2)O(2) as required for peroxidase activity. The results suggest that the proximal charge relay in peroxidases regulate the redox potential of the heme Fe but that the trans effect is a carefully balanced property that can both activate H(2)O(2) and attract ligation by the distal histidine. To understand the balance of forces that modulate peroxidase reactivity, we studied three M86 mutants, M86A, M86D, and M86E, by spectroelectrochemistry and nuclear magnetic resonance spectroscopy of (13)C- and (15)N-labeled cyanide adducts as probes of the redox potential and of the trans effect in the heme Fe, both of which can be correlated with the proximity of negative charge to the N(δ) hydrogen of the proximal histidine, consistent with an Asp-His-Fe charge relay observed in heme peroxidases.