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PDBsum entry 1vfr
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Oxidoreductase
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PDB id
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1vfr
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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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1.8 a crystal structure of the major NAD(p)h:fmn oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, Cofactor and substrate-Analog binding, And comparison with related flavoproteins.
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Authors
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H.Koike,
H.Sasaki,
T.Kobori,
S.Zenno,
K.Saigo,
M.E.Murphy,
E.T.Adman,
M.Tanokura.
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Ref.
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J Mol Biol, 1998,
280,
259-273.
[DOI no: ]
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PubMed id
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Abstract
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We have solved the crystal structure of FRase I, the major NAD(P)H:FMN
oxidoreductase of Vibrio fischeri, by the multiple isomorphous replacement
method (MIR) at 1.8 A resolution with the conventional R factor of 0.187. The
crystal structure of FRase I complexed with its competitive inhibitor,
dicoumarol, has also been solved at 2.2 A resolution with the conventional R
factor of 0.161. FRase I is a homodimer, having one FMN cofactor per subunit,
which is situated at the interface of two subunits. The overall fold can be
divided into two domains; 80% of the residues form a rigid core and the
remaining, a small flexible domain. The overall core folding is similar to those
of an NADPH-dependent flavin reductase of Vibrio harveyi (FRP) and the NADH
oxidase of Thermus thermophilus (NOX) in spite of the very low identity in amino
acid sequences (10% with FRP and 21% with NOX). 56% of alpha-carbons of FRase I
core residues could be superposed onto NOX counterparts with an r.m.s. distance
of 1.2 A. The remaining residues have relatively high B-values and may be
essential for defining the substrate specificity. Indeed, one of them, Phe124,
was found to participate in the binding of dicoumarol through stacking to one of
the rings of dicoumarol. Upon binding of dicoumarol, most of the exposed re-face
of the FMN cofactor is buried, which is consistent with the ping pong bi bi
catalytic mechanism.
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Figure 3.
Figure 3. (a) The network of hydrogen bonds between the
cofactor FMN and protein. The enzyme is drawn by a ball and
stick model. Hydrogen atoms are omitted from this Figure for
clarity. Each atom is colored according to atom type (carbon of
protein in silver, carbon of FMN in yellow). Protein residues
and N5 and N1 atoms of FMN are labeled. Hydrogen bonds are
indicated with red broken lines. (b) Electron density of FMN and
surrounding residues from a 2 F[o]−F[c]map contoured at one
σ. The FMN and its phosphate atom as well as some surrounding
residues are labeled. In this and all subsequent Figures, the
one letter code for amino acid names is used for enhanced
clarity.
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Figure 4.
Figure 4. (a) Stereoview of dicoumarol bound to FRase I,
highlighting the trans-conformation of dicoumarol such that the
corresponding keto-oxygens of the two coumarols point in
opposite directions. Residues within 4 Å from the buried
half of dicoumarol are also shown and labeled, highlighting
hydrophobic interaction with the inhibitor and protein. (b) A
chemical structure of dicoumarol.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
280,
259-273)
copyright 1998.
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Secondary reference #1
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Title
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Crystallization and preliminary crystallographic analysis of the major NAD(p)h: fmn oxidoreductase of vibrio fischeri atcc 7744.
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Authors
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H.Koike,
H.Sasaki,
M.Tanokura,
S.Zenno,
K.Saigo.
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Ref.
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J Struct Biol, 1996,
117,
70-72.
[DOI no: ]
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PubMed id
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