Crystallization and preliminary X‐ray diffraction studies of peroxidase from a fungus <i>Arthromyces ramosus</i>

Kunishima, N.; Fukuyama, Keiichi; Wakabayashi, Shigeo; Sumida, Motoo; Takaya, Masamitsu; Shibano, Yuji; Amachi, Teruo; Matsubara, Hiroshi

doi:10.1002/prot.340150213

Cited by 22 publications

(14 citation statements)

References 17 publications

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“…There is no uncertainty in the composition of samples due to the 10-20% of fungal enzyme known to contain a 'nick' between residues 303 and 304 (Kjalke et al, 1992;Kunishima et al, 1992) and, more importantly, the characterisation of recombinant CIP by NMR spectroscopy provides a sound basis for the examination of CIP mutants produced by site-directed mutagenesis.…”

Section: The Relationship Of Coprinus Peroxidase To Plant and Fungal mentioning

confidence: 99%

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NMR studies of recombinant Coprinus peroxidase and three site‐directed mutants

Veitch

Tams

Vind

et al. 1994

European Journal of Biochemistry

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Proton nuclear magnetic resonance spectroscopy has been used to characterise and compare wild-type fungal and recombinant Coprinus cinereus peroxidase (CIP) and three mutants in which Gly156 andlor Asn157 was replaced by Phe. Analysis of one-and two-dimensional NMR spectra of recombinant CIP was undertaken for comparison with the fungal enzyme and in order to establish a meaningful basis for solution studies of CIP mutants. Proton resonance assignments of haem and haem-linked residues obtained for the cyanide-ligated form of recombinant CIP revealed a high degree of spectral similarity with those of lignin and manganese-dependent peroxidases and extend previously reported NMR data for fungal CIP.The three mutants examined by NMR spectroscopy comprised site-specific substitutions made to a region of the structure believed to form part of the peroxidase haem group access channel for substrate and ligand molecules. Proton resonances of the aromatic side-chains of Phel56 and Phe157 were found to have similar spectral characteristics to those of two phenylalanine residues known to be involved in the binding of aromatic donor molecules to the plant peroxidase, horseradish peroxidase isoenzyme C. The results are discussed in the context of complementary reactivity studies on the mutants in order to develop a more detailed understanding of aromatic donor molecule binding to fungal and plant peroxidasesThe frequency with which peroxidase enzymes are being isolated and characterised from new sources far outweighs progress in our knowledge both of their three-dimensional structures and of their interactions with substrate and ligand molecules. A peroxidase in this category is that recently isolated and characterised from the ink cap basidiomycete Co-

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Section: The Relationship Of Coprinus Peroxidase To Plant and Fungal mentioning

confidence: 99%

“…Crystallographic data analysis for CIP is in progress although only a preliminary structure has been presented to date (Kunishima et al, 1992;Petersen et al, 1993a,b). Structural information for peroxidases in solution can be acquired using the techniques of nuclear magnetic resonance spectroscopy.…”

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confidence: 99%

NMR studies of recombinant Coprinus peroxidase and three site‐directed mutants

Veitch

Tams

Vind

et al. 1994

European Journal of Biochemistry

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“…Preparation of the Complex Crystals-ARP was purified and crystallized as described previously (Kunishima et al, 1993). Cyanide-derivative crystals of ARP were prepared by soaking the native ARP crystals for 2 h in mother liquor containing 1 mM KCN, 33% saturated ammonium sulfate.…”

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confidence: 99%

Crystal Structures of Cyanide- and Triiodide-bound Forms of Arthromyces ramosus Peroxidase at Different pH Values

Fukuyama

Kunishima

Amada

et al. 1995

Journal of Biological Chemistry

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The structures of the cyanide and triiodide complexes of Arthromyces ramosus peroxidase (ARP) at different pH values were investigated by x-ray crystallography in order to examine the behavior of the invariant residues of arginine (Arg-52) and distal histidine (His-56) during the enzyme reaction as well as to provide the structural basis of the active site of peroxidase. The models of the cyanide complexes at pH 7.5, 5.0, and 4.0, respectively, were refined to the R-factors of 17.8, 17.8, and 18.5% using 7.0 -1.6-Å resolution data, and those of the triiodide complexes at pH 6.5 and 5.0 refined to 16.9 and 16.8% using 7.0 -1.9-Å resolution data.The structures of the cyanide complexes at pH 7.5, 5.0, and 4.0 are identical within experimental error. Cyanide ion bound to the heme in the bent conformation rather than in the tilt conformation. Upon cyanide ion binding, the N ⑀ atom of His-56 moved toward the ion by rotation of the imidazole ring around the C ␤ -C ␥ bond, but there was little conformational change in the remaining residues. The distance between the N ⑀ atom of His-56 and the nitrogen atom of the cyanide suggests the presence of a hydrogen bond between them in the pH range investigated. In the triiodide complexes, one of the two triiodides bound to ARP was located at the distal side of the heme. When triiodide bound to ARP, unlike the rearrangement of the distal arginine of cytochrome c peroxidase that occurs on formation of the fluoride complex or compound I, the side chain of Arg-52 moved little. The conformation of the side chain of His-56, however, changed markedly. Conformational flexibility of His-56 appears to be a requisite for proton translocation from one oxygen atom to the other of HOO ؊ by acid-base catalysis to produce compound I. The iron atom in each cyanide complex (low-spin ferric) is located in the heme plane, whereas in each triiodide complex (high-spin ferric) the iron atom is displaced from the plane about 0.2 Å toward the proximal side.

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“…Enzymes-ARP was isolated from the extracellular culture medium of A. ramosus as described previously (25). All the purified proteins exhibited a single peak on Mono Q column (Amersham Pharmacia Biotech) chromatography.…”

Section: Methodsmentioning

confidence: 99%

“…The concentration of ARP was determined using ⑀ 405 of 109 mM Ϫ1 cm Ϫ1 (26). The enzyme was crystallized as described previously (25). The crystals of ARP in complex with HA were prepared by soaking the native ARP crystals for 5 h in 50 mM sodium acetate, pH 5.6, containing 20 mM HA and 35% saturated ammonium sulfate.…”

Section: Methodsmentioning

confidence: 99%

Direct Binding of Hydroxylamine to the Heme Iron ofArthromyces ramosus Peroxidase

Wariishi¹,

Nonaka²,

Johjima³

et al. 2000

Journal of Biological Chemistry

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The interaction of hydroxylamine (HA) with Arthromyces ramosus peroxidase (ARP) was investigated by kinetic, spectroscopic, and x-ray crystallographic techniques. HA inhibited the reaction of native ARP with H 2 O 2 in a competitive manner. Electron absorption and resonance Raman spectroscopic studies indicated that pentacoordinate high spin species of native ARP are converted to hexacoordinate low spin species upon the addition of HA, strongly suggesting the occurrence of a direct interaction of HA with ARP heme iron. Kinetic analysis exhibited that the apparent dissociation constant is 6.2 mM at pH 7.0 and that only one HA molecule likely binds to the vicinity of the heme. pH dependence of HA binding suggested that the nitrogen atom of HA could be involved in the interaction with the heme iron. X-ray crystallographic analysis of ARP in complex with HA at 2.0 Å resolution revealed that the electron density ascribed to HA is located in the distal pocket between the heme iron and the distal His 56 . HA seems to directly interact with the heme iron but is too far away to interact with Arg 52

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Crystallization and preliminary X‐ray diffraction studies of peroxidase from a fungus Arthromyces ramosus

Cited by 22 publications

References 17 publications

NMR studies of recombinant Coprinus peroxidase and three site‐directed mutants

NMR studies of recombinant Coprinus peroxidase and three site‐directed mutants

Crystal Structures of Cyanide- and Triiodide-bound Forms of Arthromyces ramosus Peroxidase at Different pH Values

Direct Binding of Hydroxylamine to the Heme Iron ofArthromyces ramosus Peroxidase

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