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PDBsum entry 1p4c
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Oxidoreductase
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PDB id
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1p4c
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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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High resolution structures of an oxidized and reduced flavoprotein. The water switch in a soluble form of (s)-Mandelate dehydrogenase.
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Authors
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N.Sukumar,
A.R.Dewanti,
B.Mitra,
F.S.Mathews.
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Ref.
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J Biol Chem, 2004,
279,
3749-3757.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structures of a soluble mutant of the flavoenzyme mandelate
dehydrogenase (MDH) from Pseudomonas putida and of the substrate-reduced enzyme
have been analyzed at 1.35-A resolution. The mutant (MDH-GOX2) is a fully active
chimeric enzyme in which residues 177-215 of the membrane-bound MDH are replaced
by residues 176-195 of glycolate oxidase from spinach. Both structures permit
full tracing of the polypeptide backbone chain from residues 4-356, including a
4-residue segment that was disordered in an earlier study of the oxidized
protein at 2.15 A resolution. The structures of MDH-GOX2 in the oxidized and
reduced states are virtually identical with only a slight increase in the
bending angle of the flavin ring upon reduction. The only other structural
changes within the protein interior are a 10 degrees rotation of an active site
tyrosine side chain, the loss of an active site water, and a significant
movement of six other water molecules in the active site by 0.45 to 0.78 A.
Consistent with solution studies, there is no apparent binding of either the
substrate, mandelate, or the oxidation product, benzoylformate, to the reduced
enzyme. The observed structural changes upon enzyme reduction have been
interpreted as a rearrangement of the hydrogen bonding pattern within the active
site that results from binding of a proton to the N-5 position of the anionic
hydroquinone form of the reduced flavin prosthetic group. Implications for the
low oxidase activity of the reduced enzyme are also discussed.
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Figure 4.
FIG. 4. Schematic diagram of the protein environment of FMN
in the oxidized form of MDH. Hydrogen bond distances are in
Å. Residues making hydrophobic contact to FMN are
indicated as shown in the lower right. Carbon atoms are black,
oxygen atoms red, and nitrogen atoms cyan. This diagram was
prepared using the program LIgplot (33)
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Figure 6.
FIG. 6. Comparison of the oxidized and reduced forms of
MDH-GOX2 at the enzyme active site. The side chains of Tyr26,
Tyr131, backbone of Gly81, the flavin ring, the sulfate anion,
and 7 waters of the oxidized protein are shown in atom colors
(carbon yellow, oxygen red, nitrogen light blue, and sulfur
green). Those atoms of Tyr26 and the 6 waters that show
significant movement, as well as of the sulfate anion in the
reduced enzyme, are shown in dark blue. This diagram was made
using TURBO-FRODO (21).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
3749-3757)
copyright 2004.
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Secondary reference #1
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Title
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Structure of an active soluble mutant of the membrane-Associated (s)-Mandelate dehydrogenase.
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Authors
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N.Sukumar,
Y.Xu,
D.L.Gatti,
B.Mitra,
F.S.Mathews.
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Ref.
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Biochemistry, 2001,
40,
9870-9878.
[DOI no: ]
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PubMed id
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