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The three-dimensional structure of the enzyme myeloperoxidase has been
determined by X-ray crystallography to 3 A resolution. Two heavy atom
derivatives were used to phase an initial multiple isomorphous replacement map
that was subsequently improved by solvent flattening and non-crystallographic
symmetry averaging. Crystallographic refinement gave a final model with an
R-factor of 0.257. The root-mean-square deviations from ideality for bond
lengths and angles were 0.011 A and 3.8 degrees. Two, apparently identical,
halves of the molecule are related by local dyad and covalently linked by a
single disulfide bridge. Each half-molecule consists of two polypeptide chains
of 108 and 466 amino acid residues, a heme prosthetic group, a bound calcium ion
and at least three sites of asparagine-linked glycosylation. There are six
additional intra-chain disulfide bonds, five in the large polypeptide and one in
the small. A central core region that includes the heme binding site is composed
of five alpha-helices. Regions of the larger polypeptide surrounding this core
are organized into locally folded domains in which the secondary structure is
predominantly alpha-helical with very little organized beta-sheet. A proximal
ligand to the heme iron atom has been identified as histidine 336, which is in
turn hydrogen-bonded to asparagine 421. On the distal side of the heme,
histidine 95 and arginine 239 are likely to participate directly in the
catalytic mechanism, in a manner analogous to the distal histidine and arginine
of the non-homologous enzyme cytochrome c peroxidase. The site of the covalent
linkage to the heme has been tentatively identified as glutamate 242, although
the chemical nature of the link remains uncertain. The calcium binding site has
been located in a loop comprising residues 168 to 174 together with aspartate
96. Myeloperoxidase is a member of a family of homologous mammalian peroxidases
that includes thyroid peroxidase, eosinophil peroxidase and lactoperoxidase. The
heme environment, defined by our model for myeloperoxidase, appears to be highly
conserved in these four mammalian peroxidases. Furthermore, the conservation of
all 12 cysteine residues involved in the six intra-chain disulfide bonds and the
calcium binding loop suggests that the three-dimensional structures of members
of this gene family are likely to be quite similar.
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