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PDBsum entry 1ay4
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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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Crystal structures of paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network.
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Authors
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A.Okamoto,
Y.Nakai,
H.Hayashi,
K.Hirotsu,
H.Kagamiyama.
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Ref.
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J Mol Biol, 1998,
280,
443-461.
[DOI no: ]
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PubMed id
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Abstract
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Aminotransferase reversibly catalyzes the transamination reaction by a ping-pong
bi-bi mechanism with pyridoxal 5'-phosphate (PLP) as a cofactor. Various kinds
of aminotransferases developing into catalysts for particular substrates have
been reported. Among the aminotransferases, aromatic amino acid aminotransferase
(EC 2.6.1. 57) catalyzes the transamination reaction with both acidic substrates
and aromatic substrates. To elucidate the multiple substrate recognition
mechanism, we determined the crystal structures of aromatic amino acid
aminotransferase from Paracoccus denitrificans (pdAroAT): unliganded pdAroAT,
pdAroAT in a complex with maleate as an acidic substrate analog, and pdAroAT in
a complex with 3-phenylpropionate as an aromatic substrate analog at 2.33 A, 2.
50 A and 2.30 A resolution, respectively. The pdAroAT molecule is a homo-dimer.
Each subunit has 394 amino acids and one PLP and is divided into small and large
domains. The overall structure of pdAroAT is essentially identical to that of
aspartate aminotransferase (AspAT) which catalyzes the transamination reaction
with only an acidic amino acid. On binding the acidic substrate analog, arginine
292 and 386 form end-on salt bridges with carboxylates of the analog.
Furthermore, binding of the substrate induces the domain movement to close the
active site. The recognition mechanism for the acidic substrate analog in
pdAroAT is identical to that observed in AspAT. Binding of the aromatic
substrate analog causes reorientation of the side-chain of the residues, lysine
16, asparagine 142, arginine 292* and serine 296*, and changes in the position
of water molecules in the active site to form a new hydrogen bond network in
contrast to the active site structure of pdAroAT in the complex with an acidic
substrate analog. Consequently, the rearrangement of the hydrogen bond network
can form recognition sites for both acidic and aromatic side-chains of the
substrate without a conformational change in the backbone structure in pdAroAT.
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Figure 1.
Figure 1. Ribbon drawing of a molecule of unliganded
pdAroAT viewed along the molecular dyad. α-Helices are colored
red and β-strands yellow. PLP is indicated by the
ball-and-stick model. Only in subunit A, the α-helices are
numbered and N and C-terminals are indicated by N and C,
respectively. Figure produced with MOLSCRIPT [Kraulis 1991].
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Figure 2.
Figure 2. Active site structures. PLP and inhibitor are
indicated by open bonds and water molecules by the filled
circles. (a) The active site in subunit B of the unliganded
pdAroAT; (b) the active site in subunit B of the maleate complex
of pdAroAT and (c) the active site in subunit B of the
3-phenylpropionate complex of pdAroAT. Produced with the program
ORTEP-II [Johnson 1976].
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
280,
443-461)
copyright 1998.
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Secondary reference #1
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Title
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Paracoccus denitrificans aromatic amino acid aminotransferase: a model enzyme for the study of dual substrate recognition mechanism.
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Authors
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S.Oue,
A.Okamoto,
Y.Nakai,
M.Nakahira,
T.Shibatani,
H.Hayashi,
H.Kagamiyama.
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Ref.
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J Biochem (tokyo), 1997,
121,
161-171.
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PubMed id
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