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Oxidoreductase
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PDB id
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1e3j
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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Biological process
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oxidation-reduction process
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1 term
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Biochemical function
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nucleotide binding
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4 terms
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DOI no:
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J Mol Biol
306:239-250
(2001)
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PubMed id:
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Crystal structure of the NADP(H)-dependent ketose reductase from Bemisia argentifolii at 2.3 A resolution.
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M.J.Banfield,
M.E.Salvucci,
E.N.Baker,
C.A.Smith.
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ABSTRACT
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Polyhydric alcohols are widely found in nature and can be accumulated to high
concentrations as a protection against a variety of environmental stresses. It
is only recently, however, that these molecules have been shown to be active in
protection against heat stress, specifically in the use of sorbitol by the
silverleaf whitefly, Bemisia argentifolii. We have determined the structure of
the enzyme responsible for production of sorbitol in Bemisia argentifolii,
NADP(H)-dependent ketose reductase (BaKR), to 2.3 A resolution. The structure
was solved by multiwavelength anomalous diffraction (MAD) using the anomalous
scattering from two zinc atoms bound in the structure, and was refined to an R
factor of 21.9 % (R(free)=25.1 %). BaKR belongs to the medium-chain
dehydrogenase family and its structure is the first for the sorbitol
dehydrogenase branch of this family. The enzyme is tetrameric, with the monomer
having a very similar fold to the alcohol dehydrogenases (ADHs). Although the
structure determined is for the apo form, a phosphate ion in the active site
marks the likely position for the adenyl phosphate of NADP(H). The catalytic
zinc ion is tetrahedrally coordinated to Cys41, His66, Glu67 and a water
molecule, in a modification of the zinc site usually found in ADHs. This
modified zinc site seems likely to be a conserved feature of the sorbitol
dehydrogenase sub-family. Comparisons with other members of the ADH family have
also enabled us to model a ternary complex of the enzyme, and suggest how
structural differences may influence coenzyme binding and substrate specificity
in the reduction of fructose to sorbitol.
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Selected figure(s)
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Figure 2.
Figure 2. Stereoviews showing examples of (a) the
experimental MAD/DM electron density map used to build the
initial model, and (b) the final weighted 2|F[obs]|
-|F[calc]|.f[calc] electron density map. Both maps are contoured
at 1.1s, and cover residues 171-188. The Figure was prepared
with BOBSCRIPT[45] and Raster3D. [46]
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Figure 3.
Figure 3. (a) Stereoview of the C^a trace of the final BaKR
model, with the N, C termini, and every tenth amino acid residue
labelled. (b) Schematic view of the secondary structure
arrangement in BaKR. The two zinc atoms bound in the structure
are shown in green. Figure prepared with MOLSCRIPT[47] and
Raster3D. [46]
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
306,
239-250)
copyright 2001.
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Figures were
selected
by an automated process.
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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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H.Yennawar,
M.Møller,
R.Gillilan,
and
N.Yennawar
(2011).
X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase.
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Acta Crystallogr D Biol Crystallogr, 67,
440-446.
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B.Kim,
R.P.Sullivan,
and
H.Zhao
(2010).
Cloning, characterization, and engineering of fungal L-arabinitol dehydrogenases.
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Appl Microbiol Biotechnol, 87,
1407-1414.
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D.Biswas,
M.Datt,
K.Ganesan,
and
A.K.Mondal
(2010).
Cloning and characterization of thermotolerant xylitol dehydrogenases from yeast Pichia angusta.
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Appl Microbiol Biotechnol, 88,
1311-1320.
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M.K.Tiwari,
H.J.Moon,
M.Jeya,
and
J.K.Lee
(2010).
Cloning and characterization of a thermostable xylitol dehydrogenase from Rhizobium etli CFN42.
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Appl Microbiol Biotechnol, 87,
571-581.
|
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S.Krahulec,
M.Klimacek,
and
B.Nidetzky
(2009).
Engineering of a matched pair of xylose reductase and xylitol dehydrogenase for xylose fermentation by Saccharomyces cerevisiae.
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Biotechnol J, 4,
684-694.
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S.H.Song,
N.Ahluwalia,
Y.Leduc,
L.T.Delbaere,
and
C.Vieille
(2008).
Thermotoga maritima TM0298 is a highly thermostable mannitol dehydrogenase.
|
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Appl Microbiol Biotechnol, 81,
485-495.
|
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R.Sullivan,
and
H.Zhao
(2007).
Cloning, characterization, and mutational analysis of a highly active and stable L-arabinitol 4-dehydrogenase from Neurospora crassa.
|
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Appl Microbiol Biotechnol, 77,
845-852.
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L.H.Lima,
C.G.Pinheiro,
L.M.de Moraes,
S.M.de Freitas,
and
F.A.Torres
(2006).
Xylitol dehydrogenase from Candida tropicalis: molecular cloning of the gene and structural analysis of the protein.
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Appl Microbiol Biotechnol, 73,
631-639.
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P.A.Meyer,
P.Ye,
M.Zhang,
M.H.Suh,
and
J.Fu
(2006).
Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model.
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Structure, 14,
973-982.
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PDB code:
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F.Kudo,
Y.Yamamoto,
K.Yokoyama,
T.Eguchi,
and
K.Kakinuma
(2005).
Biosynthesis of 2-deoxystreptamine by three crucial enzymes in Streptomyces fradiae NBRC 12773.
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J Antibiot (Tokyo), 58,
766-774.
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S.Watanabe,
T.Kodaki,
and
K.Makino
(2005).
Complete reversal of coenzyme specificity of xylitol dehydrogenase and increase of thermostability by the introduction of structural zinc.
|
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J Biol Chem, 280,
10340-10349.
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G.Sulzenbacher,
V.Roig-Zamboni,
F.Pagot,
S.Grisel,
A.Salomoni,
C.Valencia,
V.Campanacci,
R.Vincentelli,
M.Tegoni,
H.Eklund,
and
C.Cambillau
(2004).
Structure of Escherichia coli YhdH, a putative quinone oxidoreductase.
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Acta Crystallogr D Biol Crystallogr, 60,
1855-1862.
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PDB codes:
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M.K.Kharel,
D.B.Basnet,
H.C.Lee,
K.Liou,
J.S.Woo,
B.G.Kim,
and
J.K.Sohng
(2004).
Isolation and characterization of the tobramycin biosynthetic gene cluster from Streptomyces tenebrarius.
|
| |
FEMS Microbiol Lett, 230,
185-190.
|
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|
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|
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A.Rosell,
E.Valencia,
W.F.Ochoa,
I.Fita,
X.Parés,
and
J.Farrés
(2003).
Complete reversal of coenzyme specificity by concerted mutation of three consecutive residues in alcohol dehydrogenase.
|
| |
J Biol Chem, 278,
40573-40580.
|
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|
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|
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E.Valencia,
A.Rosell,
C.Larroy,
J.Farrés,
J.A.Biosca,
I.Fita,
X.Parés,
and
W.F.Ochoa
(2003).
Crystallization and preliminary X-ray analysis of NADP(H)-dependent alcohol dehydrogenases from Saccharomyces cerevisiae and Rana perezi.
|
| |
Acta Crystallogr D Biol Crystallogr, 59,
334-337.
|
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|
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|
|
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T.A.Pauly,
J.L.Ekstrom,
D.A.Beebe,
B.Chrunyk,
D.Cunningham,
M.Griffor,
A.Kamath,
S.E.Lee,
R.Madura,
D.Mcguire,
T.Subashi,
D.Wasilko,
P.Watts,
B.L.Mylari,
P.J.Oates,
P.D.Adams,
and
V.L.Rath
(2003).
X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase.
|
| |
Structure, 11,
1071-1085.
|
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|
PDB codes:
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|
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E.Nordling,
H.Jörnvall,
and
B.Persson
(2002).
Medium-chain dehydrogenases/reductases (MDR). Family characterizations including genome comparisons and active site modeling.
|
| |
Eur J Biochem, 269,
4267-4276.
|
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|
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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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