Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:1.11.1.7 (peroxidase)
65,474 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Molecular dynamics (MD) calculations are performed on cytochrome c peroxidase (CcP) and on horseradish peroxidase, isoenzyme C (HRP), and its substrate adduct with p-cresol. For CcP, a refinement in solution of the X-ray structure is obtained which indicates that in solution the protein structure is very similar to that in the crystal. For HRP, the X-ray structure is not available. We have generated a model of this protein based on the recently reported structure of the similar lignin peroxidase (LiP) protein. This model involves the entire system as all the amino acid residues match the sequence. This HRP model was refined through energy minimization and MD calculations. A refined structural model for HRP, for the first time involving the entire protein, is therefore now available. The tertiary structure of HRP is close to that of LiP, and also the active site in the two proteins has significantly similar structures. The well-ordered water molecules and the extensive H-bond network present in the X-ray structure of CcP is maintained in the dynamics without any constraints, indicating that the active site residues produce a field strong enough to make all these interactions quite stable. Interestingly, also in HRP a network of ordered water molecules and H-bonds is present, again without constraints. This is consistent with the similarities of the active sites in the two proteins. Finally, we have calculated the MD structure of the adduct of HRP and a substrate molecule, p-cresol. This structural model is compared with the NMR data, which are in fairly good agreement. The binding site and the protein-substrate interactions are discussed.
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PMID:Molecular dynamics studies on peroxidases: a structural model for horseradish peroxidase and a substrate adduct. 791 58

A bleachery effluent from a sulfite process pulp mill, which was extracted with alkali and treated with oxygen and hydrogen peroxide (EOP), was treated with two fungi, Trametes versicolor and Stagonospora gigaspora. Trametes versicolor did not cause any depolymerization or degradation of effluent lignins but increased the amount of chromophores, whereas S. gigaspora depolymerized the EOP lignins and caused a substantial reduction in aromatic compounds. For both fungal treatments, CuO oxidation caused a decrease in the yield of the aldehydes within the vanillyl and p-hydroxy phenol families, which was faster than the rates of decrease in the yields of the corresponding acids and ketones. However, only S. gigaspora caused changes in the pattern of the 11 characteristic lignin phenols produced by CuO oxidation, reflecting a preferential metabolism of some phenolic precursors. This fungus decreased the yield of total vanillyl phenols (V), which contributed the bulk of the 11 lignin oxidation products, from 93% initially to 59%. As a consequence, coumaryl (C), syringyl (S), and p-hydroxy phenols (P) became relatively enriched to 1.2, 6.5, and 33%, respectively. The stability of EOP-lignin constituent subunits is S > P > C > V. The two fungi differed significantly in their level of enzyme activities. In effluent-free medium, the ratio of laccase to peroxidase was higher for T. versicolor than for S. gigaspora. The presence of EOP-lignins significantly increased this ratio. No lignin peroxidase was detected but manganese peroxidase and laccase were detected during degradation activities.
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PMID:Degradability of chlorine-free bleachery effluent lignins by two fungi: effects on lignin subunit type and on polymer molecular weight. 801 7

Structural modifications of spruce liginins catalyzed by plant horseradish peroxidase (HRP) were studied. Changes in lignin structure were characterized by monomeric composition determination and hydrodynamic property analysis. Results show that HRP modifies lignin monomeric composition without alteration of polymer gel permeation pattern. This indicates that HRP and LiP have similar but different biodegradative effects.
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PMID:Is horseradish peroxidase a ligninolytic enzyme? 801 76

Disperse Yellow 3 [2-(4'-acetamidophenylazo)-4-methylphenol] (DY3) (I) is an important yellow dye used in industry and is also a carcinogen. Earlier we demonstrated that lignin-degrading cultures of white-rot basidiomycete Phanerochaete chrysosporium degrade DY3 to CO2. In this report, we have examined the degradation of DY3 and its naphthol analog, 1-(4'-acetamidophenylazo)-2-naphthol (NDY3) (II) by lignin peroxidase, horseradish peroxidase, and Mn(III)-malonate complex (a manganese peroxidase mimic). Lignin and manganese peroxidases are two extracellular peroxidase produced by ligninolytic cultures of P. chrysosporium and are involved in the degradation of lignin and various other environmental pollutants by this fungus. DY3 oxidation by peroxidases yields 4-methyl-1,2-benzoquinone (III), acetanilide (IV), and a dimer of DY3 (V) as products. NDY3 oxidation yields acetanilide (IV) and 1,2-naphthoquinone (VI). In deuterium incorporation experiments with DY3, 55-67% incorporation of deuterium from dioxane-d8 into acetanilide (IV) is observed. However, when D2O is the donor, deuterium is not incorporated into acetanilide (IV). Based on these results, a mechanism for azo dye degradation is proposed. The H2O2-oxidized forms of a peroxidase oxidize the phenolic ring of DY3, or its analogs, by two electrons to produce a carbonium ion, which is located on the carbon bearing the azo linkage. Water attacks the carbonium ion, producing an unstable intermediate which breaks down to generate 1,2-naphthoquinone (VI) or 4-methyl-1,2-benzoquinone (III) and 4-acetamido-phenyldiazene. O2, H2O2-oxidized peroxidase, or a metal ion, oxidize the phenyldiazene by one electron to produce a phenyldiazene radical, which cleaves homolytically to generate 4-acetamidophenyl radical and molecular nitrogen. The 4-acetamidophenyl radical then abstracts a hydrogen radical from the surroundings to produce acetanilide (IV). DY3 degradation by whole cultures of P. chrysosporium yields acetanilide as the major product. This suggests that lignin peroxidase and manganese peroxidase are involved in the in vivo metabolism of DY3 by P. chrysosporium.
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PMID:Peroxidase-catalyzed oxidation of azo dyes: mechanism of disperse Yellow 3 degradation. 803 Nov 41

This method was proposed earlier for measuring glucose in a peroxidase-glucose oxidase system but has not been studied for determination of manganese peroxidase (MnP) activity. The assay is based on the oxidative coupling of 3-methyl-2-benzothiazolinone hydrazone (MBTH) and 3-(dimethylamino)benzoic acid (DMAB). The reaction of MBTH and DMAB in the presence of H2O2, Mn2+, and MnP gives a deep purple-blue color with a broad absorption band with a peak at 590 nm. The extinction coefficient is high (53,000 M-1 cm-1), so low MnP activities can be detected. Lignin peroxidase and laccase, usually present in cultures of white rot fungi, gave little or no interference at the concentrations tested. However, slight interference from very high LiP activity may occur at very low MnP activity.
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PMID:Determination of manganese peroxidase activity with 3-methyl-2-benzothiazolinone hydrazone and 3-(dimethylamino)benzoic acid. 807 99

The wood-decaying fungus Trametes versicolor secretes a large number of peroxidase isozymes, presumed to partake in the degradation of lignin. From enzymic studies, two types of peroxidases have been distinguished: lignin peroxidases and manganese peroxidases. We here report the finding of a T. versicolor peroxidase gene, PG V, which displays several features not observed in previously studied peroxidase genes from white-rot fungi, such as a high number of introns (12). Eight of the 12 introns have positions equivalent to introns of peroxidase genes from another white-rot fungus, Phanerochaete chrysosporium. The gene structure of PG V appears to be primarily related to known lignin peroxidase genes, while the encoded mature 339-residue protein has several characteristics in common with manganese peroxidases. Analyses further indicate that PG V encodes a Ser instead of an Asn at a position regarded as invariant within the enzyme superfamily, with the side chain involved in hydrogen bonding with the distal His.
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PMID:A novel type of peroxidase gene from the white-rot fungus Trametes versicolor. 807 58

The structure of a recombinant peroxidase from the ink cap, Coprinus cinereus, CiP, is reported to 2.6 A resolution and refined to a R-value of 18.1%. The structure was solved by molecular replacement using the coordinates from a newly published ligninase structure. LiP. CiP crystallizes in space group P2(1)2(1)2(1) with two independent molecules in the asymmetric unit related by the vector 0.29b + 0.5c. The two CiP molecules are structurally identical; each contains two Ca2+ ions in positions equivalent to those found in the LiP structure. Two N-acetylglucosamines and one mannose residue were fitted into the density adjacent to two of the three predicted glycosylation sites. The refinement also included 40 and 41 water molecules, respectively, in the two CiP molecules. The structure of CiP displays a folding very similar to that of LiP. The active sites are almost identical in the LiP and CiP structures. CiP has a much larger opening to the active site than LiP.
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PMID:Three-dimensional structure of a recombinant peroxidase from Coprinus cinereus at 2.6 A resolution. 811 69

We demonstrate direct oxidation of ferrocytochrome c by lignin peroxidase (LiP) from the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Steady-state kinetic data fit a peroxidase ping-pong mechanism rather than an ordered bi-bi ping-pong mechanism, suggesting that the reductions of LiP compounds I and II by ferrocytochrome c are irreversible. The pH dependence of the overall reaction apparently is controlled by two factors, the pH dependence of the electron-transfer rate and the pH dependence of enzyme inactivation in the presence of H2O2. In the presence of 100 microM H2O2, veratryl alcohol (VA) significantly enhanced cytochrome c oxidation at pH 3.0 but had little effect above pH 4.5. In the presence of < 10 microM H2O2, the stimulating effect of VA on the reaction is greatly diminished. As with cytochrome c peroxidase reactions, LiP oxidation of ferrocytochrome c decreased as the ionic strength increased, implying the involvement of electrostatic interactions between the polymeric substrate and enzyme. The reaction product ferricytochrome c inhibited VA oxidation by LiP in a noncompetitive manner, suggesting that cytochrome c binds to LiP at a site different from the small aromatic substrate binding site. Recent crystallographic studies show that the heme is buried in the LiP protein and unavailable for direct interaction with polymeric substrates, suggesting that electron transfer from ferrocytochrome c to LiP occurs over a relatively long range. The role of VA in this electron-transfer reaction is discussed.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Oxidation of ferrocytochrome c by lignin peroxidase. 818 Jan 77

Horseradish peroxidase (HRP), lignin peroxidase (LiP), and Mn(III)-malonate (a manganese peroxidase mimic) oxidized 3,5-dimethyl-4-hydroxybenzenesulfonic acid (I) to 2,6-dimethyl-1,4-benzoquinone (III) and 2,6-dimethyl-1,3,4-trihydroxybenzene (IV). Only LiP was efficient at oxidizing 3,5-dimethyl-4-aminobenzenesulfonic acid (II); LiP oxidized II to 2,6-dimethyl-1,4-benzoquinone (III) and 2,6-dimethyl-3-hydroxy-1,4-benzoquinone (V). In these reactions, the H2O2-oxidized peroxidases or Mn(III)-malonate oxidized the aromatic ring by two electrons to produce a cation. Nucleophilic attack by water on the sulfonic acid bearing carbon eliminated sulfonic acid as inorganic sulfite and produced 2,6-dimethyl-1,4-benzoquinone (III). Possible mechanisms for the formation of IV and V are discussed.
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PMID:Peroxidase-catalyzed desulfonation of 3,5-dimethyl-4-hydroxy and 3,5-dimethyl-4-aminobenzenesulfonic acids. 826 18

The crystal structure of the peroxidase (donor: H2O2 oxidoreductase, EC 1.11.1.7) from the hyphomycete Arthromyces ramosus (ARP) has been determined by the multiple isomorphous replacement method and refined by the simulated annealing method to a crystallographic R-factor of 17.4% for the 19,191 reflections with F > 2 sigma F between 7.0 and 1.9 A resolution. The model includes residues 9 to 344, the heme group, two N-acetylglucosamine residues, two calcium ions and 246 water molecules. The root-mean-square deviation of bond lengths from the ideal values is 0.02 A. The mean coordinate error is estimated as 0.2 A. The electron density of the glycine-rich region of the amino-terminal eight residues was invisible. ARP has ten major and two short alpha-helices and a few short beta-strands. The overall tertiary structure of ARP is similar to that of yeast cytochrome c peroxidase (CCP) and is particularly similar to that of the lignin peroxidase (LiP) from Phanerochaete chrysosporium. Relative to CCP, ARP and LiP each have an extension of approximately 40 residues at the carboxy terminus. All eight cysteine residues in ARP form disulfide bonds (C12:C24, C23:C293, C43:C129 and C257:C322). Two calcium sites are inaccessible to solvent. The four disulfide bonds and two calcium sites, which are lacking in CCP, are conserved in ARP and LiP. The bond from Asn304C to Ala305N in ARP is the site sensitive to proteases. An Asx turn present in the Asn303 to Ala305 segment appears to orient the side-chain of Asn304 to outward from the molecule, rendering it easily trappable by pockets of proteases. The proximal heme ligand is His184 in helix F (distance of N epsilon 2 ... Fe, 2.10 A), and one of several water molecules in the distal pocket of the heme bridges the iron atom and the N epsilon 2 of His56. The orientation of the imidazole ring of the distal histidine residue relative to the heme group in ARP differs significantly from that in LiP. The access channel to the distal side of the heme of ARP is markedly wider along the heme plane than that of LiP. Many of the amino acid residues that comprise the entrance of this channel differ for ARP and LiP. This may account for the differences in substrate specificity.
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PMID:Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases. 828 54


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