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PDBsum entry 1g4x
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* Residue conservation analysis
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Enzyme class:
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E.C.2.6.1.1
- aspartate transaminase.
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Reaction:
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L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
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L-aspartate
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+
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2-oxoglutarate
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=
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oxaloacetate
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+
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L-glutamate
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Cofactor:
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Pyridoxal 5'-phosphate
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Pyridoxal 5'-phosphate
Bound ligand (Het Group name =
PLP)
matches with 93.75% similarity
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Biochemistry
40:353-360
(2001)
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PubMed id:
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Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
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H.Mizuguchi,
H.Hayashi,
K.Okada,
I.Miyahara,
K.Hirotsu,
H.Kagamiyama.
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ABSTRACT
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Systematic single and multiple replacement studies have been applied to
Escherichia coli aspartate aminotransferase to probe the electrostatic effect of
the two substrate-binding arginine residues, Arg292 and Arg386, and the
structural effect of the pyridoxal 5'-phosphate-Asn194-Arg386 hydrogen-bond
linkage system (PLP-N-R) on the pK(a) value of the Schiff base formed between
pyridoxal 5'-phosphate (PLP) and Lys258. The electrostatic effects of the two
arginine residues cannot be assessed by simple mutational studies of the
residues. PLP-N-R lowers the pK(a) value of the PLP-Lys258 Schiff base by
keeping it in the distorted conformation, which is unfavorable for protonation.
Mutation of Arg386 eliminates its hydrogen bond with Asn194 and partially
disrupts PLP-N-R, thereby relaxing the strain of the Schiff base. On the other
hand, mutation of Arg292, the large domain residue that interacts with the small
domain residue Asp15, makes the domain opening easier. Because PLP-N-R lies
between the two domains, the domain opening increases the strain of the Schiff
base. Therefore, the true electrostatic effects of Arg292 and Arg386 could be
derived from mutational analysis of the enzyme in which PLP-N-R had been
completely disrupted by the Asn194Ala mutation. Through the analyses, we could
dissect the electrostatic and structural effects of the arginine mutations on
the Schiff base pK(a). The positive charges of the two arginine residues and the
PLP-N-R-mediated strain of the Schiff base lower the Schiff base pK(a) by 0.7
and 1.7, respectively. Thus, the electrostatic effect of the arginine residues
is not as strong as has historically been thought, and this finding
substantiates our recent finding that the imine-pyridine torsion of the Schiff
base is the primary determinant (2.8 unit decrease) of the extremely low pK(a)
value of the Schiff base [Hayashi, H., Mizuguchi, H., and Kagamiyama, H. (1998)
Biochemistry 37, 15076-15085].
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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M.Höhne,
S.Schätzle,
H.Jochens,
K.Robins,
and
U.T.Bornscheuer
(2010).
Rational assignment of key motifs for function guides in silico enzyme identification.
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Nat Chem Biol,
6,
807-813.
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Y.Yoshikane,
N.Yokochi,
M.Yamasaki,
K.Mizutani,
K.Ohnishi,
B.Mikami,
H.Hayashi,
and
T.Yagi
(2008).
Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099.
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J Biol Chem,
283,
1120-1127.
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PDB codes:
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A.P.Dubnovitsky,
E.G.Kapetaniou,
and
A.C.Papageorgiou
(2005).
Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus.
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Protein Sci,
14,
97.
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PDB codes:
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A.P.Dubnovitsky,
R.B.Ravelli,
A.N.Popov,
and
A.C.Papageorgiou
(2005).
Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.
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Protein Sci,
14,
1498-1507.
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PDB codes:
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M.Goto,
R.Omi,
I.Miyahara,
A.Hosono,
H.Mizuguchi,
H.Hayashi,
H.Kagamiyama,
and
K.Hirotsu
(2004).
Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition.
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J Biol Chem,
279,
16518-16525.
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PDB codes:
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H.Hayashi,
H.Mizuguchi,
I.Miyahara,
Y.Nakajima,
K.Hirotsu,
and
H.Kagamiyama
(2003).
Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis.
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J Biol Chem,
278,
9481-9488.
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PDB codes:
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V.R.Sobrado,
M.Montemartini-Kalisz,
H.M.Kalisz,
M.C.De La Fuente,
H.J.Hecht,
and
C.Nowicki
(2003).
Involvement of conserved asparagine and arginine residues from the N-terminal region in the catalytic mechanism of rat liver and Trypanosoma cruzi tyrosine aminotransferases.
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Protein Sci,
12,
1039-1050.
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E.Deu,
K.A.Koch,
and
J.F.Kirsch
(2002).
The role of the conserved Lys68*:Glu265 intersubunit salt bridge in aspartate aminotransferase kinetics: multiple forced covariant amino acid substitutions in natural variants.
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Protein Sci,
11,
1062-1073.
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A.Matharu,
H.Hayashi,
H.Kagamiyama,
B.Maras,
and
R.A.John
(2001).
Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase.
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Eur J Biochem,
268,
1640-1645.
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H.Kagamiyama,
and
H.Hayashi
(2001).
Release of enzyme strain during catalysis reduces the activation energy barrier.
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Chem Rec,
1,
385-394.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
