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PDBsum entry 1n4u
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Oxidoreductase
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PDB id
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1n4u
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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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Atomic resolution crystallography reveals how changes in ph shape the protein microenvironment.
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Authors
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A.Y.Lyubimov,
P.I.Lario,
I.Moustafa,
A.Vrielink.
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Ref.
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Nat Chem Biol, 2006,
2,
259-264.
[DOI no: ]
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PubMed id
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Abstract
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Hydrogen atoms are a vital component of enzyme structure and function. In recent
years, atomic resolution crystallography (>or=1.2 A) has been successfully used
to investigate the role of the hydrogen atom in enzymatic catalysis. Here,
atomic resolution crystallography was used to study the effect of pH on
cholesterol oxidase from Streptomyces sp., a flavoenzyme oxidoreductase.
Crystallographic observations of the anionic oxidized flavin cofactor at basic
pH are consistent with the UV-visible absorption profile of the enzyme and
readily explain the reversible pH-dependent loss of oxidation activity.
Furthermore, a hydrogen atom, positioned at an unusually short distance from the
main chain carbonyl oxygen of Met122 at high pH, was observed, suggesting a
previously unknown mechanism of cofactor stabilization. This study shows how a
redox active site responds to changes in the enzyme's environment and how these
changes are able to influence the mechanism of enzymatic catalysis.
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Figure 4.
(a–e) Electron-density features around the imidazole ring
of His447 at pH 4.5 (a), pH 5.2 (b), pH 5.8 (c), pH 7.3 (d) and
pH 9.0 (e). (f) A view of the interactions between His447,
Asn321 and Asn323 at pH 5.2. The 2F[o] – F[c] density
(magenta) is contoured at 4.0  ,
and the sharpened F[o] – F[c] density (green) is contoured at
2.0 .
The atoms are depicted by a ball-and-stick representation. The
bifurcated hydrogen bonds formed by ND1 of His447 with the amide
groups of Asn321 and Asn323 are drawn as blue dashed lines. The
chemical structure of the histidine side chain with labeled
atoms is included.
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Figure 5.
(a) A model representing the microenvironment from pH 4.5 to
7.3, where FAD is in the neutral oxidized form and His447 is in
the imidazole form protonated at NE2. (b) A model representing
the microenvironment at pH 9.0, where the negative charge of the
imidazolate form of His447 is stabilized by interaction with
Asn321 and Asn323.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Chem Biol
(2006,
2,
259-264)
copyright 2006.
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