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PDBsum entry 2jb3
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Oxidoreductase
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PDB id
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2jb3
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References listed in PDB file
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Key reference
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Title
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The structure of a bacterial l-Amino acid oxidase from rhodococcus opacus gives new evidence for the hydride mechanism for dehydrogenation.
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Authors
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A.Faust,
K.Niefind,
W.Hummel,
D.Schomburg.
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Ref.
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J Mol Biol, 2007,
367,
234-248.
[DOI no: ]
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PubMed id
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Abstract
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l-Amino acid oxidase from Rhodococcus opacus (roLAAO) is classified as a member
of the GR(2)-family of flavin-dependent oxidoreductases according to a highly
conserved sequence motif for the cofactor binding. The monomer of the
homodimeric enzyme consists of three well-defined domains: the FAD-binding
domain corresponding to a general topology throughout the whole GR(2)-family; a
substrate-binding domain with almost the same topology as the snake venom LAAO
and a helical domain exclusively responsible for the unusual dimerisation mode
of the enzyme and not found in other members of the family so far. We describe
here high-resolution structures of the binary complex of protein and cofactor as
well as the ternary complexes of protein, cofactor and ligands. This structures
in addition to the structural knowledge of snake venom LAAO and DAAO from yeast
and pig kidney permit more insight into different steps in the reaction
mechanism of this class of enzymes. There is strong evidence for hydride
transfer as the mechanism of dehydrogenation. This mechanism appears to be
uncommon in a sense that the chemical transformation can proceed efficiently
without the involvement of amino acid functional groups. Most groups present at
the active site are involved in substrate recognition, binding and fixation,
i.e. they direct the trajectory of the interacting orbitals. In this mode of
catalysis orbital steering/interactions are the predominant factors for the
chemical step(s). A mirror-symmetrical relationship between the two
substrate-binding sites of d and l-amino acid oxidases is observed which
facilitates enantiomeric selectivity while preserving a common arrangement of
the residues in the active site. These results are of general relevance for the
mechanism of flavoproteins and lead to the proposal of a common dehydrogenation
step in the mechanism for l and d-amino acid oxidases.
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Figure 1.
Figure 1. Schematic representation of the reaction catalyzed
by amino acid oxidases.
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Figure 10.
Figure 10. (a) Schematic representation of the Michaelis
complex M1. The interactions of the active site residues with
the substrate are shown by dotted lines. l-Alanine is bound in
the zwitterionic form. (b) Schematic representation of the
product complex P1.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
367,
234-248)
copyright 2007.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray analysis of a bacterial l-Amino-Acid oxidase from rhodococcus opacus.
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Authors
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A.Faust,
B.Geueke,
K.Niefind,
W.Hummel,
D.Schomburg.
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Ref.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 2006,
62,
279-281.
[DOI no: ]
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PubMed id
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Figure 1.
Schematic representation of the reaction catalysed by LAAO.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 March 1;
62(Pt 3): 279–281. Published online 2006 February 24. doi:
10.1107/S1744309106005689. Copyright [copyright] International
Union of Crystallography 2006
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Figure 2.
(a) Crystal of the primitive orthorhombic crystal form. (b)
Crystal of the centred orthorhombic crystal form. Acta
Crystallogr Sect F Struct Biol Cryst Commun. 2006 March 1; 62(Pt
3): 279–281. Published online 2006 February 24. doi:
10.1107/S1744309106005689. Copyright [copyright] International
Union of Crystallography 2006
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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