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J. Biol. Chem., Vol. 259, Issue 21, 13027-13036, 11, 1984
BC Finzel, TL Poulos and J Kraut
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.
Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution
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