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PDBsum entry 2oov
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Oxidoreductase
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PDB id
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2oov
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References listed in PDB file
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Key reference
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Title
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Exploring molecular oxygen pathways in hansenula polymorpha copper-Containing amine oxidase.
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Authors
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B.J.Johnson,
J.Cohen,
R.W.Welford,
A.R.Pearson,
K.Schulten,
J.P.Klinman,
C.M.Wilmot.
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Ref.
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J Biol Chem, 2007,
282,
17767-17776.
[DOI no: ]
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PubMed id
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Abstract
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The accessibility of large substrates to buried enzymatic active sites is
dependent upon the utilization of proteinaceous channels. The necessity of these
channels in the case of small substrates is questionable because diffusion
through the protein matrix is often assumed. Copper amine oxidases contain a
buried protein-derived quinone cofactor and a mononuclear copper center that
catalyze the conversion of two substrates, primary amines and molecular oxygen,
to aldehydes and hydrogen peroxide, respectively. The nature of molecular oxygen
migration to the active site in the enzyme from Hansenula polymorpha is explored
using a combination of kinetic, x-ray crystallographic, and computational
approaches. A crystal structure of H. polymorpha amine oxidase in complex with
xenon gas, which serves as an experimental probe for molecular oxygen binding
sites, reveals buried regions of the enzyme suitable for transient molecular
oxygen occupation. Calculated O(2) free energy maps using copper amine oxidase
crystal structures in the absence of xenon correspond well with later
experimentally observed xenon sites in these systems, and allow the
visualization of O(2) migration routes of differing probabilities within the
protein matrix. Site-directed mutagenesis designed to block individual routes
has little effect on overall k(cat)/K(m) (O(2)), supporting multiple dynamic
pathways for molecular oxygen to reach the active site.
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Figure 1.
FIGURE 1. Reactions catalyzed by copper amine oxidases are
biogenesis (a) and catalysis (b). a, the protein derived
cofactor, TPQ, is the product of biogenesis and generates the
mature enzyme. P represents the rest of the polypeptide chain.
b, catalysis is divided into two half-reactions, reductive and
oxidative. R represents the moiety of the substrate amine, which
varies from a hydrogen atom to a polypeptide.
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Figure 5.
FIGURE 5. Comparison of CAO xenon binding sites. a, overlay
of CAO xenon sites deposited in the PDB with a monomer of the
HPAO/Xe complex. The backbone of HPAO is displayed and colored
by domain: blue stick, D1; yellow stick, D2; green ribbon, D3.
Xenon sites from individual complexes are coded by color (red,
PSAO (PDB code 1w2z); yellow, PPLO (PDB code 1rky); blue, AGAO
(PDB code 1rjo) magenta, HPAO (PDB code 2oqe)), except
surface-bound xenon sites, which are displayed as gray spheres
(31). The top inset shows the amine channel. The bottom inset
shows a proposed molecular oxygen pathway identified in this
study. The active site is shown in stick, and the copper is
shown as a green sphere. b, the HPAO D3  -sandwich domain viewed
from the dimer interface (90° rotation, cf. view in a). Only
the xenon sites in the internal D3 -sandwich and close to
the anteroom are shown. Colors are the same as in a, and arrows
indicate the direction of molecular oxygen movement to the
active site using the proposed pathway. The figure was generated
using Pymol (20).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
17767-17776)
copyright 2007.
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