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

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-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.

New Insights on the Electronic and Molecular Structure of Cyanide-Ligated Iron(III) Porphyrinates

“…[49,50,51] The IR C-N stretch provides a useful monitor of the bonding sites and ligand environment. [52,53] As has been noted for hemoproteins, the C-N stretching band in cyano-substituted iron(III) porphyrinates is very weak.…”

Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 Å resolution crystallographic study at pH 4.5

“…In the low-spin cyanide complex the iron lies in the heme plane, whereas in the high-spin triiodide complex it deviates from the plane by 0.17/~ [8].…”

“…In brief, the position of the water molecule on the distal side of the heme in peroxidases appears to be dominated by the orientation of the imidazole ring rather than by interaction with the heme. The different orientation of the imidazole ring in ARP [7,8] causes marked deviation of the water molecule from the 6th position of the heme. Generally in peroxidases the interaction between the water molecule and the heme iron appears to be weak, which is consistent with the spectroscopic evidence for CcP [10,11] and LiP [12,13].…”

“…rorhizus peroxidases were characterized by Kjalke et al [6]. Crystal structures of the native ARP, its cyanide-and triiodidebound forms, and C. cinereus peroxidase have been obtained at high resolution [7][8][9].…”

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

“…0022±2836/98/340719±21 $30.00/0 # 1998 Academic Press successfully established (Perutz, 1990), including redox-linked regulation in enzyme catalysis (Williams et al, 1997;Fu È lo È p et al, 1995;Fukuyama et al, 1995;Chen et al, 1994), no unequivocal structural basis for the cooperativity involved in electronic to protonic energy transduction has been established. This is still the case for the tetrahaem cytochromes c 3 from Desulfovibrio spp., even though considerable progress has been made in rationalising their thermodynamic properties (Santos et al, 1984;Coletta et al, 1991;Turner et al, 1994Turner et al, , 1996Park et al, 1996;Louro et al, 1996;Salgueiro et al, 1997) and high-resolution X-ray structures are available for several cytochromes c 3 in the oxidised form (Higuchi et al, 1984;Czjzek et al, 1994;Matias et al, 1996;Simo Ä es et al, 1998).…”