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PDBsum entry 1dam
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* Residue conservation analysis
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Enzyme class:
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E.C.6.3.3.3
- dethiobiotin synthase.
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Reaction:
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(7R,8S)-7,8-diammoniononanoate + CO2 + ATP = (4R,5S)-dethiobiotin + ADP + phosphate + 3 H+
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(7R,8S)-7,8-diammoniononanoate
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+
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CO2
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+
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ATP
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=
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(4R,5S)-dethiobiotin
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+
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ADP
Bound ligand (Het Group name = )
corresponds exactly
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+
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phosphate
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+
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3
×
H(+)
Bound ligand (Het Group name = )
corresponds exactly
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Protein Sci
7:2560-2566
(1998)
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PubMed id:
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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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H.Käck,
J.Sandmark,
K.J.Gibson,
G.Schneider,
Y.Lindqvist.
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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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Selected figure(s)
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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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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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J.A.Endrizzi,
H.Kim,
P.M.Anderson,
and
E.P.Baldwin
(2005).
Mechanisms of product feedback regulation and drug resistance in cytidine triphosphate synthetases from the structure of a CTP-inhibited complex.
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Biochemistry,
44,
13491-13499.
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PDB code:
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J.A.Endrizzi,
H.Kim,
P.M.Anderson,
and
E.P.Baldwin
(2004).
Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets.
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Biochemistry,
43,
6447-6463.
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PDB code:
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Madhusudan,
P.Akamine,
N.H.Xuong,
and
S.S.Taylor
(2002).
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.
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Nat Struct Biol,
9,
273-277.
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PDB code:
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K.A.Denessiouk,
and
M.S.Johnson
(2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
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Proteins,
38,
310-326.
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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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Links
