Ligand Binding to Chlorite Dismutase from <i>Magnetospirillum</i> sp.

Schutter, Amy De; Correia, H.D.; Freire, Diana Mendes; Rivas, Maria G.; Rizzi, Alberto Claudio; Santos‐Silva, Teresa; González, Pablo J.; Doorslaer, Sabine Van

doi:10.1021/acs.jpcb.5b04141

Cited by 12 publications

(19 citation statements)

References 51 publications

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“…It is noted that the g values of both LS species and particularly the HS states are slightly different from those previously reported for NdCld [37], possibly due to the use of phosphate buffer that may lead to variations in buffer pH at low temperature [38]. As has been observed for other Clds, EPR signals very similar to the LS species of NdCld, particularly LS2, reported herein have been suggested to result from binding of imidazoles or histidine residues [39,40]. The thorough EPR analysis to determine the origin of such signals in Cld from Magnetospirillum sp.…”

Section: Effect Of Disruption Of Proximal H-bonding On the Spin Statecontrasting

confidence: 70%

“…Although the spectral features of the LS state are reminiscent of an N-ligated haeme iron (Figure 3; Supplementary Table S1), its origin is unclear, as previously reported for Cld from Magnetospirillum sp. ; the LS ligand possibly being stabilized by H-bonding with the flexible distal arginine [40]. In fact, it is known that the distal Arg is able to change between two conformations, either pointing towards or away from the haeme iron [24][25][26].…”

Section: Discussionmentioning

confidence: 99%

“…The thorough EPR analysis to determine the origin of such signals in Cld from Magnetospirillum sp. by van Doorslaer excluded histidine ligation but could not offer a conclusive assignment of the LS species [40]. It was suggested that a buffer molecule may lead to the formation of the LS species, possibly stabilized by H-bonding with the distal Arg residue, though this proposal could not be confirmed.…”

Section: Effect Of Disruption Of Proximal H-bonding On the Spin Statementioning

confidence: 96%

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From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

et al. 2016

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SynopsisChlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from 'Candidatus Nitrospira defluvii' (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV-vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure-function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.

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Section: Effect Of Disruption Of Proximal H-bonding On the Spin Statecontrasting

confidence: 70%

Section: Discussionmentioning

confidence: 99%

Section: Effect Of Disruption Of Proximal H-bonding On the Spin Statementioning

confidence: 96%

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From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

et al. 2016

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“…The EPR spectra of chlorite dismutase from Magnetospirillum sp. showed different HS and LS features that were influenced by the purification method ( 30 ), NaCl excess ( 30 ), pH, and aging ( 31 ). On the contrary, only one HS species was found in the dimeric chlorite dismutase from Cyanothece sp.…”

Section: Discussionmentioning

confidence: 99%

Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage

Pfanzagl

Nys

Bellei

et al. 2018

Journal of Biological Chemistry

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117

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Dye-decolorizing peroxidases (DyPs) represent the most recently classified hydrogen peroxide–dependent heme peroxidase family. Although widely distributed with more than 5000 annotated genes and hailed for their biotechnological potential, detailed biochemical characterization of their reaction mechanism remains limited. Here, we present the high-resolution crystal structures of WT B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) (1.6 Å) and the variants D143A (1.3 Å), R232A (1.9 Å), and D143A/R232A (1.1 Å). We demonstrate the impact of elimination of the DyP-typical, distal residues Asp-143 and Arg-232 on (i) the spectral and redox properties, (ii) the kinetics of heterolytic cleavage of hydrogen peroxide, (iii) the formation of the low-spin cyanide complex, and (iv) the stability and reactivity of an oxoiron(IV)porphyrin π-cation radical (Compound I). Structural and functional studies reveal that the distal aspartate is responsible for deprotonation of H2O2 and for the poor oxidation capacity of Compound I. Elimination of the distal arginine promotes a collapse of the distal heme cavity, including blocking of one access channel and a conformational change of the catalytic aspartate. We also provide evidence of formation of an oxoiron(IV)-type Compound II in KpDyP with absorbance maxima at 418, 527, and 553 nm. In summary, a reaction mechanism of the peroxidase cycle of B-class DyPs is proposed. Our observations challenge the idea that peroxidase activity toward conventional aromatic substrates is related to the physiological roles of B-class DyPs.

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“… 51 In structures of cyanide–Cld complexes, the conserved distal arginine binds to ligands like cyanide, azide, and thiocyanate. 13 , 14 , 54 In HemQs from Firmicutes, this arginine is missing and exchanged with a glutamine, which, because of the chemical nature of its side chain, has a lower capacity to electrostatically attract and bind the negatively charged ions.…”

Section: Discussionmentioning

confidence: 99%

Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ

et al. 2016

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Recently, a novel pathway for heme b biosynthesis in Gram-positive bacteria has been proposed. The final poorly understood step is catalyzed by an enzyme called HemQ and includes two decarboxylation reactions leading from coproheme to heme b. Coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. In the study presented here, we focus on HemQs from Listeria monocytogenes (LmHemQ) and Staphylococcus aureus (SaHemQ) recombinantly produced as apoproteins in Escherichia coli. We demonstrate the rapid and two-phase uptake of coproheme by both apo forms and the significant differences in thermal stability of the apo forms, coproheme-HemQ and heme b-HemQ. Reduction of ferric high-spin coproheme-HemQ to the ferrous form is shown to be enthalpically favored but entropically disfavored with standard reduction potentials of −205 ± 3 mV for LmHemQ and −207 ± 3 mV for SaHemQ versus the standard hydrogen electrode at pH 7.0. Redox thermodynamics suggests the presence of a pronounced H-bonding network and restricted solvent mobility in the heme cavity. Binding of cyanide to the sixth coproheme position is monophasic but relatively slow (∼1 × 104 M–1 s–1). On the basis of the available structures of apo-HemQ and modeling of both loaded forms, molecular dynamics simulation allowed analysis of the interaction of coproheme and heme b with the protein as well as the role of the flexibility at the proximal heme cavity and the substrate access channel for coproheme binding and heme b release. Obtained data are discussed with respect to the proposed function of HemQ in monoderm bacteria.

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Ligand Binding to Chlorite Dismutase from Magnetospirillum sp.

Cited by 12 publications

References 51 publications

From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

From chlorite dismutase towards HemQ–the role of the proximal H-bonding network in haeme binding

Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage

Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ

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