PDBsum entry 1arv

Peroxidase (donor:h2o2 oxidoreductase)

PDB id: 1arv

Contents

Protein chain

336 a.a. *

Ligands

NAG-NAG

CYN

HEM

Metals

_CA ×2

Waters ×300

* Residue conservation analysis

PDB id:

1arv

Name:

Peroxidase (donor:h2o2 oxidoreductase)

Title:

Crystal structures of cyanide-and triiodide-bound forms of arthromyces ramosus peroxidase at different ph values. Perturbations of active site residues and their implication in enzyme catalysis

Structure:

Peroxidase. Chain: a. Other_details: ph 5.0

Source:

'Arthromyces ramosus'. Organism_taxid: 5451

Resolution:

1.60Å R-factor: 0.178

Authors:

K.Fukuyama,N.Kunishima,F.Amada

Key ref:

K.Fukuyama et al. (1995). Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis. J Biol Chem, 270, 21884-21892. PubMed id: 7665612

Date:

25-Apr-95 Release date: 29-Jan-96

Protein chain

P28313  (PER_ARTRA) -  Peroxidase from Arthromyces ramosus

Seq: 364 a.a.

Struc: 336 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.7 - peroxidase.
• Reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O
• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

J Biol Chem 270:21884-21892 (1995)

PubMed id: 7665612

Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis.

K.Fukuyama, N.Kunishima, F.Amada, T.Kubota, H.Matsubara.

ABSTRACT

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-A 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-A 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 epsilon atom of His-56 moved toward the ion by rotation of the imidazole ring around the C beta-C gamma bond, but there was little conformational change in the remaining residues. The distance between the N epsilon 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 A toward the proximal side.