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.
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.
Fukuyama
K
K
Department of Biology, Faculty of Science, Osaka University, Japan.
Kunishima
N
N
Amada
F
F
Kubota
T
T
Matsubara
H
H
D000595:Amino Acid Sequence; D001120:Arginine; D001665:Binding Sites; D003196:Computer Graphics; D018360:Crystallography, X-Ray / Q000379:methods; D005583:Fourier Analysis; D006418:Heme / Q000032:analysis; D006639:Histidine; D006863:Hydrogen-Ion Concentration; D007454:Iodides; D003904:Mitosporic Fungi / Q000201:enzymology*; D008958:Models, Molecular; D010504:Periodic Acid; D010544:Peroxidases / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism*; D017680:Potassium Compounds; D011190:Potassium Cyanide
D007454:Iodides; D017680:Potassium Compounds; D010504:Periodic Acid; D006418:Heme; D006639:Histidine; D001120:Arginine; D010544:Peroxidases; D011190:Potassium Cyanide; C037192:potassium periodate