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See detailCrystal structure and high-temperature properties of the Ruddlesden–Popper phases Sr3−xYx(Fe1.25Ni0.75)O7−δ (0≤x≤0.75)
Samain, Louise ULiege; Amshoff, Philipp; Biendicho, Jordi J. et al

in Journal of Solid State Chemistry (2015), 227

Abstract Ruddlesden–Popper n=2 member phases Sr3−xYxFe1.25Ni0.75O7−δ, 0≤x≤0.75, have been investigated by X-ray and neutron powder diffraction, thermogravimetry and Mössbauer spectroscopy. Both samples as ... [more ▼]

Abstract Ruddlesden–Popper n=2 member phases Sr3−xYxFe1.25Ni0.75O7−δ, 0≤x≤0.75, have been investigated by X-ray and neutron powder diffraction, thermogravimetry and Mössbauer spectroscopy. Both samples as-prepared at 1300°C under N2(g) flow and samples subsequently air-annealed at 900°C were studied. The as-prepared x=0.75 phase is highly oxygen deficient with δ=1, the O1 atom site being vacant, and the Fe3+/Ni2+ ions having a square pyramidal coordination. For as-prepared phases with lower x values, the Mössbauer spectral data are in good agreement with the presence of both 5- and 4-coordinated Fe3+ ions, implying in addition a partial occupancy of the O3 atom sites that form the basal plane of the square pyramid. The air-annealed x=0.75 sample has a δ value of 0.61(1) and the structure has Fe/Ni ions in both square pyramids and octahedra. Mössbauer spectroscopy shows the phase to contain only Fe3+, implying that all Ni is present as Ni3+. Air-annealed phases with lower x values are found to contain both Fe3+ and Fe4+. For both the as-prepared and the air-annealed samples, the Y3+ cations are found to be mainly located in the perovskite block. The high-temperature thermal expansion of as-prepared and air-annealed x=0.75 phases were investigated by high-temperature X-ray diffraction and dilatometry and the linear thermal expansion coefficient determined to be 14.4ppmK−1. Electrical conductivity measurements showed that the air-annealed samples have higher conductivity than the as-prepared ones. [less ▲]

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See detailCrystal Structure and Kinetic Analysis of the Class B3 Di-Zinc Metallo-β-Lactamase LRA-12 from an Alaskan Soil Metagenome
Rodríguez, María Margarita; Herman, Raphaël ULiege; Ghiglione, Barbara et al

in PLoS ONE (in press)

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See detailCrystal Structure and Local Disorder in Modern and Ancient Prussian Blue Pigments
Samain, Louise ULiege; Martinetto, Pauline; Bordet, Pierre et al

Poster (2012, June 06)

The necessity of understanding degradation and alteration processes in a painting's materials is well established for preservation and art history issues. The task is however complex because of the highly ... [more ▼]

The necessity of understanding degradation and alteration processes in a painting's materials is well established for preservation and art history issues. The task is however complex because of the highly heterogeneous character of a paint layer, which consists of a mixture of pigments and a binder on a support. In this context we focus on a particular pigment, Prussian blue. Prussian blue is a hydrated ferric ferrocyanide complex, first synthesized in 1704 in Berlin. It has been widely used by artists until the 1970's. However reports of discoloration had already appeared in eighteenth and nineteenth century books. To date, little attention has been devoted to the understanding of the degradation processes of Prussian blue in paint layers. The preparation methods of Prussian blue were rapidly recognized as a contributory factor in the fading of the pigment because they lead to the introduction of impurities in its structure. The crystal structure of Prussian blue is notoriously complex because of the presence of vacancies and local disorder. Unresolved questions about the crystal structure of the soluble variety of Prussian blue, i.e., Prussian blue containing alkali cations, are still found in the literature. We reproduced modern and ancient preparation methods of Prussian blue and analyzed the obtained pigments by high-energy powder diffraction at the beamline ID11, ESRF, Grenoble and at the beamline CRISTAL, Soleil, Paris. The crystal structure of soluble Prussian blue was reviewed by Rietveld refinement and appears to contain approximately a quart of iron(II) sites vacant, similarly to the well-known insoluble crystal structure. The refinement of the pair distribution function extracted from the total scattering signal revealed a local structure different from the average one. The local arrangements are best described by combining three different substructures with different numbers of vacancies and vary upon the type of synthesis. The PDF analysis also evidenced the formation of nanocrystalline ferrihydrite and alumina hydrate in Prussian blue pigments synthesized according to eighteenth-century recipes. The local disorder and the presence of an undesirable iron compound in Prussian blue can help to better understand the degradation mechanisms in paint layers containing this pigment. [less ▲]

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See detailCrystal structure of 7-chloro-3-isopropoxy-4H-1,2,4-benzothiadiazine 1,1-dioxide monohydrate, C10H13CIN2O4S H2O
Dupont, L.; Boverie, S.; Pirotte, Bernard ULiege et al

in Zeitschrift für Kristallographie. New Crystal Structures (2005), NCS 220

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See detailCrystal structure of 7-chloro-3-isopropylamino-4H-1,2,4-benzothiadiazine 1,1-dioxide, C10H12CIN3O2S
Dupont, L.; Pirotte, Bernard ULiege; De Tullio, Pascal ULiege

in Zeitschrift für Kristallographie. New Crystal Structures (2005), NCS 220

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See detailCrystal structure of 7-chloro-3-isopropylsulfanyl-4H-1,2,4-benzothiadiazine 1,1-dioxide, C10H11CIN2O2S2
Dupont, L.; Boverie, S.; De Tullio, Pascal ULiege et al

in Zeitschrift für Kristallographie. New Crystal Structures (2005), NCS 220

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See detailCrystal structure of a cold-adapted class C beta-lactamase.
Michaux, Catherine; Massant, Jan; Kerff, Frédéric ULiege et al

in FEBS Journal (2008), 275(8), 1687-97

In this study, the crystal structure of a class C beta-lactamase from a psychrophilic organism, Pseudomonas fluorescens, has been refined to 2.2 A resolution. It is one of the few solved crystal ... [more ▼]

In this study, the crystal structure of a class C beta-lactamase from a psychrophilic organism, Pseudomonas fluorescens, has been refined to 2.2 A resolution. It is one of the few solved crystal structures of psychrophilic proteins. The structure was compared with those of homologous mesophilic enzymes and of another, modeled, psychrophilic protein. The elucidation of the 3D structure of this enzyme provides additional insights into the features involved in cold adaptation. Structure comparison of the psychrophilic and mesophilic beta-lactamases shows that electrostatics seems to play a major role in low-temperature adaptation, with a lower total number of ionic interactions for cold enzymes. The psychrophilic enzymes are also characterized by a decreased number of hydrogen bonds, a lower content of prolines, and a lower percentage of arginines in comparison with lysines. All these features make the structure more flexible so that the enzyme can behave as an efficient catalyst at low temperatures. [less ▲]

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See detailCrystal structure of a complex between the Actinomadura R39 DD-peptidase and a peptidoglycan-mimetic boronate inhibitor: interpretation of a transition state analogue in terms of catalytic mechanism.
Dzhekieva, Liudmila; Rocaboy, Mathieu ULiege; Kerff, Frédéric ULiege et al

in Biochemistry (2010), 49(30), 6411-9

The Actinomadura R39 DD-peptidase is a bacterial low molecular weight class C penicillin-binding protein. It has previously been shown to catalyze hydrolysis and aminolysis of small D-alanyl-D-alanine ... [more ▼]

The Actinomadura R39 DD-peptidase is a bacterial low molecular weight class C penicillin-binding protein. It has previously been shown to catalyze hydrolysis and aminolysis of small D-alanyl-D-alanine terminating peptides, especially those with a side chain that mimics the amino terminus of the stem peptide precursor to the bacterial cell wall. This paper describes the synthesis of (D-alpha-aminopimelylamino)-D-1-ethylboronic acid, designed to be a peptidoglycan-mimetic transition state analogue inhibitor of the R39 DD-peptidase. The boronate was found to be a potent inhibitor of the peptidase with a K(i) value of 32 +/- 6 nM. Since it binds some 30 times more strongly than the analogous peptide substrate, the boronate may well be a transition state analogue. A crystal structure of the inhibitory complex shows the boronate covalently bound to the nucleophilic active site Ser 49. The aminopimelyl side chain is bound into the site previously identified as specific for this moiety. One boronate oxygen is held in the oxyanion hole; the other, occupying the leaving group site of acylation or the nucleophile site of deacylation, appears to be hydrogen-bonded to the hydroxyl group of Ser 298. The Ser 49 oxygen appears to be hydrogen bonded to Lys 52. If it is assumed that this structure does resemble a high-energy tetrahedral intermediate in catalysis, it seems likely that Ser 298 participates as part of a proton transfer chain initiated by Lys 52 or Lys 410 as the primary proton donor/acceptor. The structure, therefore, supports a particular class of mechanism that employs this proton transfer device. [less ▲]

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See detailCrystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.
Bompard-Gilles, C.; Remaut, H.; Villeret, V. et al

in Structure (2000), 8(9), 971-80

BACKGROUND: beta-Lactam compounds are the most widely used antibiotics. They inactivate bacterial DD-transpeptidases, also called penicillin-binding proteins (PBPs), involved in cell-wall biosynthesis ... [more ▼]

BACKGROUND: beta-Lactam compounds are the most widely used antibiotics. They inactivate bacterial DD-transpeptidases, also called penicillin-binding proteins (PBPs), involved in cell-wall biosynthesis. The most common bacterial resistance mechanism against beta-lactam compounds is the synthesis of beta-lactamases that hydrolyse beta-lactam rings. These enzymes are believed to have evolved from cell-wall DD-peptidases. Understanding the biochemical and mechanistic features of the beta-lactam targets is crucial because of the increasing number of resistant bacteria. DAP is a D-aminopeptidase produced by Ochrobactrum anthropi. It is inhibited by various beta-lactam compounds and shares approximately 25% sequence identity with the R61 DD-carboxypeptidase and the class C beta-lactamases. RESULTS: The crystal structure of DAP has been determined to 1.9 A resolution using the multiple isomorphous replacement (MIR) method. The enzyme folds into three domains, A, B and C. Domain A, which contains conserved catalytic residues, has the classical fold of serine beta-lactamases, whereas domains B and C are both antiparallel eight-stranded beta barrels. A loop of domain C protrudes into the substrate-binding site of the enzyme. CONCLUSIONS: Comparison of the biochemical properties and the structure of DAP with PBPs and serine beta-lactamases shows that although the catalytic site of the enzyme is very similar to that of beta-lactamases, its substrate and inhibitor specificity rests on residues of domain C. DAP is a new member of the family of penicillin-recognizing proteins (PRPs) and, at the present time, its enzymatic specificity is clearly unique. [less ▲]

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See detailCrystal structure of a dimeric oxidized form of human peroxiredoxin 5
Evrard, Christine ULiege; Capron, Arnaud; Marchand, Cécile et al

in Journal of Molecular Biology (2004), 337

Peroxiredoxin 5 is the last discovered mammalian member of an ubiquitous family of peroxidases widely distributed among prokaryotes and eukaryotes. Mammalian peroxiredoxin 5 has been recently classified ... [more ▼]

Peroxiredoxin 5 is the last discovered mammalian member of an ubiquitous family of peroxidases widely distributed among prokaryotes and eukaryotes. Mammalian peroxiredoxin 5 has been recently classified as an atypical 2-Cys peroxiredoxin due to the presence of a conserved peroxidatic N-terminal cysteine (Cys47) and an unconserved resolving C-terminal cysteine residue (Cys151) forming an intramolecular disulfide intermediate in the oxidized enzyme. We have recently reported the crystal structure of human peroxiredoxin 5 in its reduced form. Here, a new crystal form of human peroxiredoxin 5 is described at 2.0 Ǻ resolution. The asymmetric unit contains three polypeptide chains. Surprisingly, beside two reduced chains, the third one is oxidized although the enzyme was crystallized under initial reducing conditions in presence of 1 mM 1,4-dithio-DL-threitol. The oxidized polypeptide chain forms an homodimer with a symmetry related one through intermolecular disulfide bonds between Cys47 and Cys151. The formation of these disulfide bonds is accompanied by the partial unwinding of the N-terminal parts of the a2 helix, which in the reduced form, contains the peroxidatic Cys47 and the α6 helix, which is sequentially close to the resolving residue Cys151. In each monomer of the oxidized chain, the C-terminal part including the α6 helix is completely reorganized and is isolated from the rest of the protein on an extended arm. In the oxidized dimer, the arm belonging to the first monomer now appears at the surface of the second subunit and vice versa. [less ▲]

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See detailThe Crystal Structure Of A Penicilloyl-Serine Transferase Of Intermediate Penicillin Sensitivity - The Dd-Transpeptidase Of Streptomyces K15
Fonze, E.; Vermeire, M.; Nguyen-Disteche, M. et al

in Journal of Biological Chemistry (1999), 274(31), 21853-60

The serine DD-transpeptidase/penicillin-binding protein of Streptomyces K15 catalyzes peptide bond formation in a way that mimics the penicillin-sensitive peptide cross-linking reaction involved in ... [more ▼]

The serine DD-transpeptidase/penicillin-binding protein of Streptomyces K15 catalyzes peptide bond formation in a way that mimics the penicillin-sensitive peptide cross-linking reaction involved in bacterial cell wall peptidoglycan assembly. The Streptomyces K15 enzyme is peculiar in that it can be considered as an intermediate between classical penicillin-binding proteins, for which benzylpenicillin is a very efficient inactivator, and the resistant penicillin-binding proteins that have a low penicillin affinity. With its moderate penicillin sensitivity, the Streptomyces K15 DD-transpeptidase would be helpful in the understanding of the structure-activity relationship of this penicillin-recognizing protein superfamily. The structure of the Streptomyces K15 enzyme has been determined by x-ray crystallography at 2.0-A resolution and refined to an R-factor of 18.6%. The fold adopted by this 262-amino acid polypeptide generates a two-domain structure that is close to those of class A beta-lactamases. However, the Streptomyces K15 enzyme has two particular structural features. It lacks the amino-terminal alpha-helix found in the other penicilloyl-serine transferases, and it exhibits, at its surface, an additional four-stranded beta-sheet. These two characteristics might serve to anchor the enzyme in the plasma membrane. The overall topology of the catalytic pocket of the Streptomyces K15 enzyme is also comparable to that of the class A beta-lactamases, except that the Omega-loop, which bears the essential catalytic Glu(166) residue in the class A beta-lactamases, is entirely modified. This loop adopts a conformation similar to those found in the Streptomyces R61 DD-carboxypeptidase and class C beta-lactamases, with no equivalent acidic residue. [less ▲]

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See detailCrystal structure of arsenuranospathite from Rabejac, Lodève, France
Dal Bo, Fabrice ULiege; Hatert, Frédéric ULiege; Baijot, Maxime ULiege et al

in European Journal of Mineralogy (2015), 27

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See detailCrystal structure of bassetite and saléeite: new insight into autunite-group minerals
Dal Bo, Fabrice ULiege; Hatert, Frédéric ULiege; Mees, Florias et al

in European Journal of Mineralogy (2016)

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See detailThe crystal structure of bertossaite, CaLi2[Al4(PO4)4(OH,F)4]
Hatert, Frédéric ULiege; Lefèvre, Pierre; Fransolet, André-Mathieu ULiege

in Canadian Mineralogist (2011), 49

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See detailCrystal structure of BRL 42715, C6-(N1-methyl-1,2,3-triazolylmethylene)penem, in complex with Enterobacter cloacae 908R beta-lactamase: evidence for a stereoselective mechanism from docking studies.
Michaux, Catherine; Charlier, Paulette ULiege; Frère, Jean-Marie ULiege et al

in Journal of the American Chemical Society (2005), 127(10), 3262-3

BRL 42715, C6-(N1-methyl-1,2,3-triazolylmethylene)penem, is an active-site-directed inactivator of bacterial beta-lactamases. The crystal structure of Enterobacter cloacae 908R class C beta-lactamase in ... [more ▼]

BRL 42715, C6-(N1-methyl-1,2,3-triazolylmethylene)penem, is an active-site-directed inactivator of bacterial beta-lactamases. The crystal structure of Enterobacter cloacae 908R class C beta-lactamase in complex with BRL 42715, docking, and energy minimization studies explain stereoselectivity of the binding of C6-(heterocyclic methylene)penems against class C beta-lactamase. [less ▲]

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See detailCrystal structure of cholera toxin B-pentamer bound to receptor GM1 pentasaccharide
Merritt, E. A.; Sarfaty, S.; van den Akker, F. et al

in Protein Science : A Publication of the Protein Society (1994), 3(2), 166-75

Cholera toxin (CT) is an AB5 hexameric protein responsible for the symptoms produced by Vibrio cholerae infection. In the first step of cell intoxication, the B-pentamer of the toxin binds specifically to ... [more ▼]

Cholera toxin (CT) is an AB5 hexameric protein responsible for the symptoms produced by Vibrio cholerae infection. In the first step of cell intoxication, the B-pentamer of the toxin binds specifically to the branched pentasaccharide moiety of ganglioside GM1 on the surface of target human intestinal epithelial cells. We present here the crystal structure of the cholera toxin B-pentamer complexed with the GM1 pentasaccharide. Each receptor binding site on the toxin is found to lie primarily within a single B-subunit, with a single solvent-mediated hydrogen bond from residue Gly 33 of an adjacent subunit. The large majority of interactions between the receptor and the toxin involve the 2 terminal sugars of GM1, galactose and sialic acid, with a smaller contribution from the N-acetyl galactosamine residue. The binding of GM1 to cholera toxin thus resembles a 2-fingered grip: the Gal(beta 1-3)GalNAc moiety representing the "forefinger" and the sialic acid representing the "thumb." The residues forming the binding site are conserved between cholera toxin and the homologous heat-labile enterotoxin from Escherichia coli, with the sole exception of His 13. Some reported differences in the binding affinity of the 2 toxins for gangliosides other than GM1 may be rationalized by sequence differences at this residue. The CTB5:GM1 pentasaccharide complex described here provides a detailed view of a protein:ganglioside specific binding interaction, and as such is of interest not only for understanding cholera pathogenesis and for the design of drugs and development of vaccines but also for modeling other protein:ganglioside interactions such as those involved in GM1-mediated signal transduction. [less ▲]

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See detailCrystal structure of Enterobacter cloacae 908R class C beta-lactamase bound to iodo-acetamido-phenyl boronic acid, a transition-state analogue
Wouters, J.; Fonze, E.; Vermeire, M. et al

in Cellular and Molecular Life Sciences (2003), 60(8), 1764-1773

The structures of the, class C beta-lactamase from Enterobacter cloacae 908R alone and in complex with a baronic acid transition-state analogue were determined by X-ray crystallography at 2.1 and 2.3 ... [more ▼]

The structures of the, class C beta-lactamase from Enterobacter cloacae 908R alone and in complex with a baronic acid transition-state analogue were determined by X-ray crystallography at 2.1 and 2.3 Angstrom, respectively. The structure of the enzyme resembles those of other class C beta-lactamases. The structure of the. complex with the transition-state analogue, iodo-acetamido-phenyl boronic acid, shows that the inhibitor is covalently, bound to the active-site serine (Ser64). Binding of the inhibitor within the active site is compared with previously determined structures of complexes with other class C enzymes. The structure of the boronic acid adduct indicates ways to improve the affinity of this class of inhibitors. This structure of 908R class C beta-lactamase in complex with a transitionstate analogue provides further insights into the mechanism of action of these hydrolases. [less ▲]

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See detailCrystal structure of extended-spectrum beta-lactamase Toho-1: Insights into the molecular mechanism for catalytic reaction and substrate specificity expansion
Ibuka, A. S.; Ishii, Y.; Galleni, Moreno ULiege et al

in Biochemistry (2003), 42(36), 10634-10643

The crystallographic structure of the class A beta-lactamase Toho-1, an extended-spectrum beta-lactamase with potent activity against expanded-spectrum cephems, has been determined at 1.65 Angstrom ... [more ▼]

The crystallographic structure of the class A beta-lactamase Toho-1, an extended-spectrum beta-lactamase with potent activity against expanded-spectrum cephems, has been determined at 1.65 Angstrom resolution. The result reveals that the Lys73 side chain can adopt two alternative conformations. The predominant conformation of Lys73 is different from that observed in the E166A mutant, indicating that removal of the Glu166 side chain changes the conformation of the Lys73 side chain and thus the interaction between Lys73 and Glu166. The Lys73 side chain would play an important role in proton relay, switching its conformation from one to the other depending on the circumstances. The electron density map also implies possible rotation of Ser237. Comparison of the Toho-1 structure with the structure of other class A beta-lactamases shows that the hydroxyl group of Ser237 is likely to rotate through interaction with the carboxyl group of the substrate. Another peculiarity is the existence of three sulfate ions positioned in or near the substrate-binding cavity. One of these sulfate ions is tightly bound to the active center, while the other two are held by a region of positive charge formed by two arginine residues, Arg274 and Arg276. This positively charged region is speculated to represent a pseudo-binding site of the beta-lactam antibiotics, presumably catching the methoxyimino group of the third-generation cephems prior to proper binding in the substrate-binding cleft for hydrolysis. This high-resolution structure, together with detailed kinetic analysis of Toho-1, provides a new hypothesis for the catalytic mechanism and substrate specificity of Toho-1. [less ▲]

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See detailCrystal Structure of Human Peroxiredoxin 5, a Novel Type of Mammalian Peroxiredoxin at 1.5 Ǻ Resolution
Declercq, Jean-Paul; Evrard, Christine ULiege; Clippe, André et al

in Journal of Molecular Biology (2001), 311

The peroxiredoxins define an emerging family of peroxidases able to reduce hydrogen peroxide and alkyl hydroperoxides with the use of reducing equivalents derived from thiol-containing donor molecules ... [more ▼]

The peroxiredoxins define an emerging family of peroxidases able to reduce hydrogen peroxide and alkyl hydroperoxides with the use of reducing equivalents derived from thiol-containing donor molecules such as thioredoxin, glutathione, trypanothione and AhpF. Peroxiredoxins have been identified in prokaryotes as well as in eukaryotes. Peroxiredoxin 5 (PRDX5) is a novel type of mammalian thioredoxin peroxidase widely expressed in tissues and located cellularly to mitochondria, peroxisomes and cytosol. Functionally, PRDX5 has been implicated in antioxidant protective mechanisms as well as in signal transduction in cells. We report here the 1.5 Ǻ resolution crystal structure of human PRDX5 in its reduced form. The crystal structure reveals that PRDX5 presents a thioredoxin-like domain. Interestingly, the crystal structure shows also that PRDX5 does not form a dimer like other mammalian members of the peroxiredoxin family. In the reduced form of PRDX5, Cys47 and Cys151 are distant of 13.8 Ǻ although these two cysteine residues are thought to be involved in peroxide reductase activity by forming an intramolecular disul®de intermediate in the oxidized enzyme. These data suggest that the enzyme would necessitate a conformational change to form a disulfide bond between catalytic Cys47 and Cys151 upon oxidation according to proposed peroxide reduction mechanisms. Moreover, the presence of a benzoate ion, a hydroxyl radical scavenger, was noted close to the active-site pocket. The possible role of benzoate in the antioxidant activity of PRDX5 is discussed. [less ▲]

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