Structural and spectroscopic characterisation of a heme peroxidase from sorghum

Nnamchi, Chukwudi I.; Parkin, Gary; Efimov, Igor; Basran, Jaswir; Kwon, Hanna; Svistunenko, Dimitri A.; Agirre, Jon; Okolo, B. N.; Moneke, Anene N.; Nwanguma, Bennett C.; Moody, Peter C.E.; Raven, Emma Lloyd

doi:10.1007/s00775-015-1313-z

Cited by 21 publications

(34 citation statements)

References 25 publications

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“…The heme group (grey), with δ-meso edge (red), is fixed by His-170 in the active site. ( c ) Clustal Omega ( ) was used for multiple sequence alignment of HRP [ 40 ], membrane-bound peroxidases and soluble peroxidases that were used as templates for modelling of structures shown in Figure 2 [ 36 , 41 , 42 , 43 ]. Active sites (yellow), calcium binding-sites (grey), conserved cysteine residues for formation of disulfide bridges (blue), transmembrane domains (bold and underlined), signal peptides (italic).…”

Section: Figurementioning

confidence: 99%

Membrane-Bound Class III Peroxidases: Unexpected Enzymes with Exciting Functions

Lüthje

Martínez-Cortés

2018

IJMS

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Class III peroxidases are heme-containing proteins of the secretory pathway with a high redundance and versatile functions. Many soluble peroxidases have been characterized in great detail, whereas only a few studies exist on membrane-bound isoenzymes. Membrane localization of class III peroxidases has been demonstrated for tonoplast, plasma membrane and detergent resistant membrane fractions of different plant species. In silico analysis revealed transmembrane domains for about half of the class III peroxidases that are encoded by the maize (Zea mays) genome. Similar results have been found for other species like thale-cress (Arabidopsis thaliana), barrel medic (Medicago truncatula) and rice (Oryza sativa). Besides this, soluble peroxidases interact with tonoplast and plasma membranes by protein–protein interaction. The topology, spatiotemporal organization, molecular and biological functions of membrane-bound class III peroxidases are discussed. Besides a function in membrane protection and/or membrane repair, additional functions have been supported by experimental data and phylogenetics.

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Section: Figurementioning

confidence: 99%

Membrane-Bound Class III Peroxidases: Unexpected Enzymes with Exciting Functions

Lüthje

Martínez-Cortés

2018

IJMS

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“…Top, plant N-glycans typically show 1-3 core-linked fucose and 1-2 xylose linked to the first mannose sugar. In the figure, a diagram of one of the glycans found in a haem peroxidase from sorghum (PDB entry 5aog; Nnamchi et al, 2016). Middle, a complete, unprocessed high-mannose N-glycan linked to a glycosyl hydrolase enzyme from the fungus Aspergillus fumigatus (PDB entry 5fji; .…”

Section: Glycosylation: An Underdog Goes Mainstreammentioning

confidence: 99%

Strategies for carbohydrate model building, refinement and validation

Agirre

2017

Acta Crystallogr D Struct Biol

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Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein–sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.

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“…Higher-order iron-oxo species, such as Fe IV =O which is implicated in the HCO mechanism, 79 and other similar species were not observed in these case. 80,81 Interestingly, a clear formation of heme-oxy was not observed in Fe II - or Cu I -Fe B Mb(Fe II ) because the nonheme Fe II or Cu I donates an electron to heme-bound oxygen. 13 This electron transfer thus leads to more highly reactive heme-oxygen species, such as peroxy which were unable to be detected.…”

Section: Resultsmentioning

confidence: 99%

Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism

Reed¹,

Shi

Zhu

et al. 2017

J. Am. Chem. Soc.

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The presence of nonheme metal, such as copper and iron, in the heme-copper oxidase (HCO) superfamily is critical to the enzymatic activity of reducing O2 to H2O, but the exact mechanism the nonheme metal ion uses to confer and fine-tune the activity remains to be understood. We report that manganese and cobalt can bind to the same nonheme site and confer HCO activity in a heme-nonheme biosynthetic model in myoglobin. While the initial rates of O2 reduction by the Mn, Fe and Co derivatives are similar, the percentage of reaction active species formation are 7%, 4% and 1% and the total turnovers are 5.1 ± 1.1, 13.4 ± 0.7, and 82.5 ± 2.5, respectively. These results correlate with the trends of nonheme metal-binding dissociation constants (35 μM, 22 μM and 9 μM) closely, suggesting that tighter metal binding can prevent ROS release from the active site, lessen damage to the protein, and produce higher total turnover numbers. Detailed spectroscopic, electrochemical, and computational studies found no evidence of redox cycling of manganese or cobalt in the enzymatic reactions, and suggest that structural and electronic effects related to the presence of different nonheme metals lead to observed differences in reactivity. This study of the roles of nonheme metal ions beyond the Cu and Fe found in native enzymes has provided deeper insights into nature’s choice of metal ion, and reaction mechanism, and allows for finer control of the enzymatic activity, which is a basis for design of efficient catalysts for oxygen reduction reaction for fuel cells.

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Structural and spectroscopic characterisation of a heme peroxidase from sorghum

Cited by 21 publications

References 25 publications

Membrane-Bound Class III Peroxidases: Unexpected Enzymes with Exciting Functions

Membrane-Bound Class III Peroxidases: Unexpected Enzymes with Exciting Functions

Strategies for carbohydrate model building, refinement and validation

Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism

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