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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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