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Title
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Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution.
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Authors
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B.C.Finzel,
T.L.Poulos,
J.Kraut.
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Ref.
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J Biol Chem, 1984,
259,
13027-13036.
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PubMed id
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Abstract
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The crystal structure of cytochrome c peroxidase (EC 1.11.1.5) has been refined
to an R factor of 0.20 computed for all reflections to 1.7 A. The refined
molecular model includes 263 bound water molecules and allows for x-ray
scattering by amorphous solvent. The mean positional error in atomic coordinates
is estimated to lie between 0.12 and 0.21 A. Two factors are identified which
may account for the ability of the enzyme to stabilize high-oxidation states of
the heme iron during catalysis: 1) the proximal histidine forms a hydrogen bond
with a buried aspartic acid side chain, Asp-235; and 2) the heme environment is
more polar than in the cytochromes c or globins, owing to the presence of the
partially buried side-chain of Arg-48 and five water molecules bound in close
proximity to the heme. Two of these occupy the presumed peroxide-binding site.
Two candidates are likely for the side chain that is oxidized to a free radical
during formation of Compound I: 1) Trp-51, which rests 3.3 A above the heme
plane in close proximity (2.7 A) to the sixth coordination position; and 2)
Met-172, which is 3.7 A from the heme. Nucleophilic stabilization of the
methionyl cation radical may be possible via Asp-235. His-181 is found to lie
coplanar with the heme in a niche between the two propionates near the suspected
cytochrome c-binding site. A network of hydrogen bonds involving this histidine
may provide a preferred pathway for electron transfer between hemes.
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