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PDBsum entry 1dam
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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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Crystal structure of two quaternary complexes of dethiobiotin synthetase, Enzyme-Mgadp-Alf3-Diaminopelargonic acid and enzyme-Mgadp-Dethiobiotin-Phosphate; implications for catalysis.
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Authors
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H.Käck,
J.Sandmark,
K.J.Gibson,
G.Schneider,
Y.Lindqvist.
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Ref.
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Protein Sci, 1998,
7,
2560-2566.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structures of two complexes of dethiobiotin synthetase,
enzyme-diaminopelargonic acid-MgADP-AlF3 and enzyme-dethiobiotin-MgADP-Pi,
respectively, have been determined to 1.8 A resolution. In dethiobiotin
synthetase, AlF3 together with carbamylated diaminopelargonic acid mimics the
phosphorylated reaction intermediate rather than the transition state complex
for phosphoryl transfer. Observed differences in the binding of substrate,
diaminopelargonic acid, and the product, dethiobiotin, suggest considerable
displacements of substrate atoms during the ring closure step of the catalytic
reaction. In both complexes, two metal ions are observed at the active site,
providing evidence for a two-metal mechanism for this enzyme.
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Figure 1.
Fig. 1. Reaction scheme for DTBS
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Figure 2.
ig. 2. Initial differenceelectrondensity(contoured at 3r) attheactivesitein (A) the and (B) the
DTBS-MgADP-DTB-Picomplex.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1998,
7,
2560-2566)
copyright 1998.
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Secondary reference #1
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Title
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Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
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Authors
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H.Käck,
K.J.Gibson,
Y.Lindqvist,
G.Schneider.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
5495-5500.
[DOI no: ]
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PubMed id
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Figure 4.
Fig. 4. Polar interactions of the substrate (a) and the
reaction intermediate (b) with protein atoms at the active site
of DTBS. Hydrogen bonds (cutoff distance 3.2 Å) are shown
with dotted lines. Coordination bonds from atoms of the protein
and the substrate/reaction intermediate to the Mg2+ ions are
included.
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Figure 6.
Fig. 6. Refined structure of the metal sites of the
complex of DTBS with ADP and a reaction intermediate, the mixed
carbamic-phosphoric acid anhydride. Golden spheres indicate
magnesium ions, and red spheres indicate solvent molecules.
Coordination bonds are shown by dotted lines.
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Secondary reference #2
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Title
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Crystal structure of an ATP-Dependent carboxylase, Dethiobiotin synthetase, At 1.65 a resolution.
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Authors
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W.Huang,
Y.Lindqvist,
G.Schneider,
K.J.Gibson,
D.Flint,
G.Lorimer.
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Ref.
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Structure, 1994,
2,
407-414.
[DOI no: ]
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PubMed id
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Figure 9.
Figure 9. Schematic view of the dimer of dethiobiotin
synthetase. The color scheme is that used in Figure 4 and Figure
5. Conserved side chains at the subunit–subunit interface are
included in ball- and-stick representation (for details see
text). The picture was generated with the program MOLSCRIPT
[21]. Figure 9. Schematic view of the dimer of dethiobiotin
synthetase. The color scheme is that used in [3]Figure 4 and
[4]Figure 5. Conserved side chains at the subunit–subunit
interface are included in ball- and-stick representation (for
details see text). The picture was generated with the program
MOLSCRIPT [[5]21].
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Figure 11.
Figure 11. Schematic view of the active site of dethiobiotin
synthetase. The color scheme is that used for Figure 4 and
Figure 5. Conserved polar residues in the vicinity of the
suggested binding site of the γ -phosphate of ATP are shown.
The picture was generated with the program MOLSCRIPT [21].
Figure 11. Schematic view of the active site of dethiobiotin
synthetase. The color scheme is that used for [3]Figure 4 and
[4]Figure 5. Conserved polar residues in the vicinity of the
suggested binding site of the γ -phosphate of ATP are shown.
The picture was generated with the program MOLSCRIPT [[5]21].
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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