 |
PDBsum entry 1gin
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Crystal structures of adenylosuccinate synthetase from escherichia coli complexed with gdp, Imp hadacidin, No3-, And mg2+.
|
|
|
Authors
|
|
B.W.Poland,
H.J.Fromm,
R.B.Honzatko.
|
|
|
Ref.
|
|
J Mol Biol, 1996,
264,
1013-1027.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
|
|
|
|
Abstract
|
|
|
Crystal structures of adenylosuccinate synthetase from Esherichia coli complexed
with Mg2+, IMP, GDP, NO3- and hadacidin at 298 and 100 K have been refined to
R-factors of 0.188 and 0.206 against data to 2.8 A and 2.5 A resolution,
respectively. Conformational changes of up to 9 A relative to the unligated
enzyme occur in loops that bind to Mg2+, GDP, IMP and hadacidin. Mg2+ binds
directly to GDP, NO3-, hadacidin and the protein, but is only five-coordinated.
Asp13, which approaches, but does not occupy the sixth coordination site of
Mg2+, hydrogen bonds to N1 of IMP. The nitrogen atom of NO3- is approximately
2.7 A from O6 of IMP, reflecting a strong electrostatic interaction between the
electron-deficient nitrogen atom and the electron-rich O6. The spatial
relationships between GDP, NO3- and Mg2+ suggest an interaction between the
beta,gamma-bridging oxygen atom of GTP and Mg2+ in the enzyme-substrate complex.
His41 hydrogen bonds to the beta-phosphate group of GDP and approaches bound
NO3-. The aldehyde group of hadacidin coordinates to the Mg2+, while its
carboxyl group interacts with backbone amide groups 299 to 303 and the
side-chain of Arg303. The 5'-phosphate group of IMP interacts with Asn38,
Thr129, Thr239 and Arg143 (from a monomer related by 2-fold symmetry). A
mechanism is proposed for the two-step reaction governed by the synthetase, in
which His41 and Asp13 are essential catalytic side-chains.
|
|
|
|
|
|
|
|
Figure 1.
Figure 1. A diagram of hadacidin showing chirality,
covalent linkages and names of atoms (in parentheses).
Groups within circles are represented by single, unified
atoms in refinement.
|
|
Figure 8.
Figure 8. Stereoview of Mg
2+
in
the active site of the ligated syn-
thetase at 100 K. Broken lines rep-
resent donor-acceptor interactions,
coordinate bonds or significant elec-
trostatic interactions less than 3.2 Å .
Ligands are drawn with bold lines.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
264,
1013-1027)
copyright 1996.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Refined crystal structures of unligated adenylosuccinate synthetase from escherichia coli.
|
|
|
Authors
|
|
M.M.Silva,
B.W.Poland,
C.R.Hoffman,
H.J.Fromm,
R.B.Honzatko.
|
|
|
Ref.
|
|
J Mol Biol, 1995,
254,
431-446.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 1.
Figure 1. Amino acid sequence used in the refinement
of unligated crystal structures of the synthetase.
|
|
Figure 8.
Figure 8. Identification of the active site of the synthetase (top) by the location of IMP and GDP in a preliminary
crystal structure, (middle) by directed mutation, and (bottom) by the mapping of conserved residues of synthetases from
bacteria, yeast and mammals. Drawing by MOLSCRIPT (Kraulis, 1991).
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from Elsevier
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Crystal structure of adenylosuccinate synthetase from escherichia coli. Evidence for convergent evolution of gtp-Binding domains.
|
|
|
Authors
|
|
B.W.Poland,
M.M.Silva,
M.A.Serra,
Y.Cho,
K.H.Kim,
E.M.Harris,
R.B.Honzatko.
|
|
|
Ref.
|
|
J Biol Chem, 1993,
268,
25334-25342.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
