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PDBsum entry 1qwm
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Oxidoreductase
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PDB id
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1qwm
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of helicobacter pylori catalase, With and without formic acid bound, At 1.6 a resolution.
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Authors
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P.C.Loewen,
X.Carpena,
C.Rovira,
A.Ivancich,
R.Perez-Luque,
R.Haas,
S.Odenbreit,
P.Nicholls,
I.Fita.
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Ref.
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Biochemistry, 2004,
43,
3089-3103.
[DOI no: ]
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PubMed id
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Abstract
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Helicobacter pylori produces one monofunctional catalase, encoded by katA
(hp0875). The crystal structure of H. pylori catalase (HPC) has been determined
and refined at 1.6 A with crystallographic agreement factors R and R(free) of
17.4 and 21.9%, respectively. The crystal exhibits P2(1)2(1)2 space group
symmetry and contains two protein subunits in the asymmetric unit. The core
structure of the HPC subunit, including the disposition of a heme b prosthetic
group, is closely related to those of other catalases, although it appears to be
the only clade III catalase that has been characterized that does not bind
NADPH. The heme iron in one subunit of the native enzyme appears to be
covalently modified, possibly with a perhydroxy or dioxygen group in a compound
III-like structure. Formic acid is known to bind in the active site of
catalases, promoting the breakdown of reaction intermediates compound I and
compound II. The structure of an HPC crystal soaked with sodium formate at pH
5.6 has also been determined to 1.6 A (with R and R(free) values of 18.1 and
20.7%, respectively), revealing at least 36 separate formate or formic acid
residues in the HPC dimer. In turn, the number of water molecules refined into
the models decreased from 1016 in the native enzyme to 938 in the
formate-treated enzyme. Extra density, interpreted as azide, is found in a
location of both structures that involves interaction with all four subunits in
the tetramer. Electron paramagnetic resonance spectra confirm that azide does
not bind as a ligand of the iron and that formate does bind in the heme pocket.
The stability of the formate or formic acid molecule found inside the heme
distal pocket has been investigated by calculations based on density functional
theory.
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