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PDBsum entry 1knp
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Oxidoreductase
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PDB id
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1knp
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Contents |
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* Residue conservation analysis
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Enzyme class 2:
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E.C.1.4.3.16
- L-aspartate oxidase.
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Reaction:
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L-aspartate + O2 = iminosuccinate + H2O2
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L-aspartate
Bound ligand (Het Group name = )
matches with 88.89% similarity
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+
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O2
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=
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iminosuccinate
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+
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H2O2
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Cofactor:
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FAD
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FAD
Bound ligand (Het Group name =
FAD)
corresponds exactly
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Enzyme class 3:
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E.C.1.5.99.-
- ?????
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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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
41:3018-3024
(2002)
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PubMed id:
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Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis.
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R.T.Bossi,
A.Negri,
G.Tedeschi,
A.Mattevi.
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ABSTRACT
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L-Aspartate oxidase (Laspo) catalyzes the conversion of L-Asp to iminoaspartate,
the first step in the de novo biosynthesis of NAD(+). This bacterial pathway
represents a potential drug target since it is absent in mammals. The Laspo
R386L mutant was crystallized in the FAD-bound catalytically competent form and
its three-dimensional structure determined at 2.5 A resolution in both the
native state and in complex with succinate. Comparison of the R386L holoprotein
with the wild-type apoenzyme [Mattevi, A., Tedeschi, G., Bacchella, L., Coda,
A., Negri, A., and Ronchi, S. (1999) Structure 7, 745-756] reveals that cofactor
incorporation leads to the ordering of two polypeptide segments (residues 44-53
and 104-141) and to a 27 degree rotation of the capping domain. This motion
results in the formation of the active site cavity, located at the interface
between the capping domain and the FAD-binding domain. The structure of the
succinate complex indicates that the cavity surface is decorated by two clusters
of H-bond donors that anchor the ligand carboxylates. Moreover, Glu121, which is
strictly conserved among Laspo sequences, is positioned to interact with the
L-Asp alpha-amino group. The architecture of the active site of the Laspo
holoenzyme is remarkably similar to that of respiratory fumarate reductases,
providing strong evidence for a common mechanism of catalysis in Laspo and
flavoproteins of the succinate dehydrogenase/fumarate reductase family. This
implies that Laspo is mechanistically distinct from other flavin-dependent amino
acid oxidases, such as the prototypical D-amino acid oxidase.
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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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E.A.Bushnell,
E.Erdtman,
J.Llano,
L.A.Eriksson,
and
J.W.Gauld
(2011).
The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase.
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J Comput Chem,
32,
822-834.
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T.Kurihara
(2011).
A mechanistic analysis of enzymatic degradation of organohalogen compounds.
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Biosci Biotechnol Biochem,
75,
189-198.
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A.Miura,
M.Kameya,
H.Arai,
M.Ishii,
and
Y.Igarashi
(2008).
A soluble NADH-dependent fumarate reductase in the reductive tricarboxylic acid cycle of Hydrogenobacter thermophilus TK-6.
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J Bacteriol,
190,
7170-7177.
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M.W.van der Kamp,
F.Perruccio,
and
A.J.Mulholland
(2008).
High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase.
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Chem Commun (Camb),
(),
1874-1876.
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T.M.Tomasiak,
E.Maklashina,
G.Cecchini,
and
T.M.Iverson
(2008).
A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II.
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J Biol Chem,
283,
15460-15468.
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PDB code:
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Y.O.You,
and
W.A.van der Donk
(2007).
Mechanistic investigations of the dehydration reaction of lacticin 481 synthetase using site-directed mutagenesis.
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Biochemistry,
46,
5991-6000.
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J.A.Imlay
(2006).
Iron-sulphur clusters and the problem with oxygen.
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Mol Microbiol,
59,
1073-1082.
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A.Kurata,
T.Kurihara,
H.Kamachi,
and
N.Esaki
(2005).
2-Haloacrylate reductase, a novel enzyme of the medium chain dehydrogenase/reductase superfamily that catalyzes the reduction of a carbon-carbon double bond of unsaturated organohalogen compounds.
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J Biol Chem,
280,
20286-20291.
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H.Sakuraba,
H.Tsuge,
K.Yoneda,
N.Katunuma,
and
T.Ohshima
(2005).
Crystal structure of the NAD biosynthetic enzyme quinolinate synthase.
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J Biol Chem,
280,
26645-26648.
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PDB code:
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G.Cecchini
(2003).
Function and structure of complex II of the respiratory chain.
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Annu Rev Biochem,
72,
77.
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M.H.Hefti,
J.Vervoort,
and
W.J.van Berkel
(2003).
Deflavination and reconstitution of flavoproteins.
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Eur J Biochem,
270,
4227-4242.
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K.R.Messner,
and
J.A.Imlay
(2002).
Mechanism of superoxide and hydrogen peroxide formation by fumarate reductase, succinate dehydrogenase, and aspartate oxidase.
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J Biol Chem,
277,
42563-42571.
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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
code is
shown on the right.
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Links
