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PDBsum entry 1bfd
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References listed in PDB file
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Key reference
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Title
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The crystal structure of benzoylformate decarboxylase at 1.6 a resolution: diversity of catalytic residues in thiamin diphosphate-Dependent enzymes.
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Authors
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M.S.Hasson,
A.Muscate,
M.J.Mcleish,
L.S.Polovnikova,
J.A.Gerlt,
G.L.Kenyon,
G.A.Petsko,
D.Ringe.
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Ref.
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Biochemistry, 1998,
37,
9918-9930.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the thiamin diphosphate (ThDP)-dependent enzyme
benzoylformate decarboxylase (BFD), the third enzyme in the mandelate pathway of
Pseudomonas putida, has been solved by multiple isomorphous replacement at 1.6 A
resolution and refined to an R-factor of 15.0% (free R = 18.6%). The structure
of BFD has been compared to that of other ThDP-dependent enzymes, including
pyruvate decarboxylase. The overall architecture of BFD resembles that of the
other family members, and cofactor- and metal-binding residues are well
conserved. Surprisingly, there is no conservation of active-site residues not
directly bound to the cofactor. The position of functional groups in the active
site may be conserved, however. Three classes of metal ions have been identified
in the BFD crystal structure: Ca2+ bound to the cofactor in each subunit, Mg2+
on a 2-fold axis of the tetramer, and Ca2+ at a crystal contact. The structure
includes a non-proline cis-peptide bond and an unusually long and regular
polyproline type II helix that mediates the main contact between tetramers in
the crystal. The high-quality electron-density map allowed the correction of
errors totaling more than 10% of the amino acid sequence, which had been
predicted from the reported sequence of the mdlC gene. Analysis of the BFD
structure suggests that requirements for activation of the cofactor, the nature
of the reaction intermediates, and architectural considerations relating to the
protein fold have been dominant forces in the evolution of ThDP-dependent
enzymes.
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Secondary reference #1
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Title
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Purification and crystallization of benzoylformate decarboxylase.
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Authors
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M.S.Hasson,
A.Muscate,
G.T.Henehan,
P.F.Guidinger,
G.A.Petsko,
D.Ringe,
G.L.Kenyon.
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Ref.
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Protein Sci, 1995,
4,
955-959.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Analysisofthepurification of benzoylformatedecarboxylase
by SDS-PAGE.Aliquosoftheenzymepreparationaftereachstagein
thepurificationwereseparated by denaturing gel electrophoresis. he
amount of eachsampleloaded was normalizedfortheamount of ben-
zoylformatedecarboxylasepresentinit.Lane I, crudeextract;lane 2,
samplesafterammoniumsulfatefractionation;lane 3. Affi-Bluecol-
umn;lane 4, FastSepharosecolumn;lan 5, phenyl Sepharosecolumn;
andlane 6, molecularweightstandards.Numbersattherightindicate
themolecularmassofthemarkers in kilodaltons.
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Figure 3.
Fig. 3. Crystals of benzoylformate decarboxylase. The crystal
pictured is approximately 0.3 mmin length.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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Secondary reference #2
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Title
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Structural and kinetic analysis of catalysis by a thiamin diphosphate-Dependent enzyme, Benzoylformate decarboxylase.
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Authors
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E.S.Polovnikova,
M.J.Mcleish,
E.A.Sergienko,
J.T.Burgner,
N.L.Anderson,
A.K.Bera,
F.Jordan,
G.L.Kenyon,
M.S.Hasson.
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Ref.
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Biochemistry, 2003,
42,
1820-1830.
[DOI no: ]
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PubMed id
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