Independent evolution of four heme peroxidase superfamilies

Zámocký, Marcel; Hofbauer, Stefan; Schaffner, Irene; Gasselhuber, Bernhard; Nicolussi, Andrea; Soudi, Monika; Pirker, Katharina F.; Furtmüller, Paul G.; Obinger, Christian

doi:10.1016/j.abb.2014.12.025

Cited by 203 publications

(204 citation statements)

References 65 publications

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“…We also demonstrated that the availability of a HS ligand can compensate this instability and render the enzyme properties wild-type-like. Since the overall subunit fold of proteins within the peroxidaseCld family (structural CDE superfamily) is highly conserved [1,2,60] and Cld-like proteins (HemQs) and Clds share similar active site architecture, our study has provided a better insight into the biochemistry of Cld-like proteins. The most striking difference between Cld-like proteins, HemQs, and functional Clds is the catalytic distal arginine which is fully conserved only in the latter.…”

Section: Discussionmentioning

confidence: 99%

“…Mutational studies on Clds from 'Candidatus Nitrospira defluvii' (NdCld) [12,23] and from D. aromatica (DaCld) [24] revealed that the distal arginine -the only charged residue on the distal side of the haeme -is very important for chlorite degradation. It is conserved in Clds and DyPs, whereas in HemQs alanine, leucine, glutamine or serine can be found at this position ( Figure 1A) [1,11,12]. HemQs do not show any chlorite degrading activity [4][5][6].…”

Section: Introductionmentioning

confidence: 99%

“…In contrast with HemQ, many structural and functional data about Clds have been published in the last decade, which might also contribute to a better understanding of the structure-function relationships in HemQ [1,11,12]. This includes Clds from perchlorate reducing bacteria (Azospira oryzae GR-1, Ideonella dechloratans, Dechloromonas aromatica, Pseudomonas chloritidismutans, Magnetospirillum sp.)…”

Section: Introductionmentioning

confidence: 99%

“…The peroxidase-chlorite dismutase superfamily (CDE structural superfamily) comprises chlorite dismutases (Clds), chlorite dismutase-like (Cld-like) proteins (HemQs in Gram-positive bacteria) and dye-decolourizing peroxidases (DyPs) [1,2]. Although distinct enzymatic reactions can be assigned to Clds (degradation of chlorite to chloride and dioxygen) and DyPs (H 2 O 2 -mediated one-electron oxidation reactions of various aromatic compounds), knowledge about the biochemical and physiological function of Cld-like proteins is only fragmentary at present.…”

Section: Introductionmentioning

confidence: 99%

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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: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…1 They play a key role in lignin degradation enabling the fungal decay of wood and other lignocellulosic biomass for carbon recycling in land ecosystems. 2,3 Enzymatic delignification and lignin modification are of high biotechnological interest, having multiple potential applications from paper pulp manufacturing to the production of biofuels, chemicals and added value products in lignocellulose biorefineries, where all biomass constituents should be used.…”

Section: Introductionmentioning

confidence: 99%

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

et al. 2017

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Abstract:Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of lignin in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.3

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Chloroplastic ascorbate peroxidases targeted to stroma or thylakoid membrane: The chicken or egg dilemma

et al. 2022

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Ascorbate peroxidases (APXs) are heme peroxidases that remove hydrogen peroxide in different subcellular compartments with concomitant ascorbate cycling. Here, we analysed and discussed phylogenetic and molecular features of the APX family. Ancient APX originated as a soluble stromal enzyme, and early during plant evolution, acquired both chloroplast‐targeting and mitochondrion‐targeting sequences and an alternative splicing mechanism whereby it could be expressed as a soluble or thylakoid membrane‐bound enzyme. Later, independent duplication and neofunctionalization events in some angiosperm groups resulted in individual genes encoding stromal, thylakoidal and mitochondrial isoforms. These data reaffirm the complexity of plant antioxidant defenses that allow diverse plant species to acquire new means to adapt to changing environmental conditions.

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Independent evolution of four heme peroxidase superfamilies

Abstract: Graphical abstract

Cited by 203 publications

References 65 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

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases

Chloroplastic ascorbate peroxidases targeted to stroma or thylakoid membrane: The chicken or egg dilemma

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