 |
PDBsum entry 1lcd
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Gene regulation/DNA
|
PDB id
|
|
|
|
1lcd
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structure of the complex of lac repressor headpiece and an 11 base-Pair half-Operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics.
|
|
|
Authors
|
|
V.P.Chuprina,
J.A.Rullmann,
R.M.Lamerichs,
J.H.Van boom,
R.Boelens,
R.Kaptein.
|
|
|
Ref.
|
|
J Mol Biol, 1993,
234,
446-462.
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The structure of the complex of lac repressor headpiece and an 11 base-pair lac
half-operator has been determined by NMR spectroscopy and restrained Molecular
Dynamics calculations. In total 508 distances were derived from two-dimensional
nuclear Overhauser enhancement measurements, 260 of which are within the
headpiece, 212 within the operator and 36 between operator and headpiece. An
equilibrium restrained Molecular Dynamics calculation of the complex in aqueous
solution, spanning 85 picoseconds, has been used to analyze the structure.
Configuration sampling by an annealing procedure has been undertaken as well in
order to estimate the precision of the structure determination. Our data confirm
the results of previous two-dimensional NMR studies that the orientation of the
recognition helix of lac repressor in the major groove of DNA with respect to
the operator dyad axis is opposite to the orientation found in complexes of
other DNA binding proteins of the helix-turn-helix class. We find a number of
tight contacts between the protein and the operator that are in agreement with
the available genetic and biochemical data. The anchoring of lac headpiece on
the operator is similar to that of other repressors. Other features are unique
for lac headpiece: relative few direct hydrogen bonds between side-chains and
bases; extensive apolar contacts; many direct and water-bridged contacts to
phosphates from residues in or close to the recognition helix. Overall, an
interconnected set of interactions is observed, involving base-specific
contacts, phosphate contacts, intra-protein and water-bridged hydrogen bonds.
Several of these interactions appear to be dynamic, i.e. fluctuating in time,
rather than static.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Assignment of the 1h-Nmr spectrum of a lac repressor headpiece-Operator complex in h2o and identification of noes. Consequences for protein-Dna interaction.
|
|
|
Authors
|
|
R.M.Lamerichs,
R.Boelens,
G.A.Van der marel,
J.H.Van boom,
R.Kaptein.
|
|
|
Ref.
|
|
Eur J Biochem, 1990,
194,
629-637.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Two-Dimensional nmr study of a protein-Dna complex. Lac repressor headpiece-Operator interaction.
|
|
|
Authors
|
|
R.Kaptein,
R.M.Lamerichs,
R.Boelens,
J.A.Rullmann.
|
|
|
Ref.
|
|
Biochem Pharmacol, 1990,
40,
89-96.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #3
|
|
|
Title
|
|
H nmr study of a complex between the lac repressor headpiece and a 22 base pair symmetric lac operator.
|
|
|
Authors
|
|
R.M.Lamerichs,
R.Boelens,
G.A.Van der marel,
J.H.Van boom,
R.Kaptein,
F.Buck,
B.Fera,
H.Rüterjans.
|
|
|
Ref.
|
|
Biochemistry, 1989,
28,
2985-2991.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #4
|
|
|
Title
|
|
Nmr based docking studies of lac repressor headpiece on a lac operator fragment
|
|
|
Authors
|
|
J.A.C.Rullmann,
R.Boelens,
R.Kaptein.
|
|
|
Ref.
|
|
ucla symp mol cell biol ,, 1989,
95,
11.
|
|
|
|
Secondary reference #5
|
|
|
Title
|
|
The interaction of lac repressor headpiece with its operator: an nmr view.
|
|
|
Authors
|
|
R.Boelens,
R.M.Lamerichs,
J.A.Rullmann,
J.H.Van boom,
R.Kaptein.
|
|
|
Ref.
|
|
Protein Seq Data Anal, 1988,
1,
487-498.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #6
|
|
|
Title
|
|
Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from escherichia coli.
|
|
|
Authors
|
|
J.De vlieg,
R.M.Scheek,
W.F.Van gunsteren,
H.J.Berendsen,
R.Kaptein,
J.Thomason.
|
|
|
Ref.
|
|
Proteins, 1988,
3,
209-218.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #7
|
|
|
Title
|
|
A two-Dimensional nmr study of the complex of lac repressor headpiece with a 14 base pair lac operator fragment
|
|
|
Authors
|
|
R.Boelens,
R.M.Scheek,
R.M.J.N.Lamerichs,
J.De vlieg,
J.H.Van boom,
R.Kaptein.
|
|
|
Ref.
|
|
nato asi ser ,ser a, 1987,
137,
191.
|
|
|
|
Secondary reference #8
|
|
|
Title
|
|
Complex of lac repressor headpiece with a 14 base-Pair lac operator fragment studied by two-Dimensional nuclear magnetic resonance.
|
|
|
Authors
|
|
R.Boelens,
R.M.Scheek,
J.H.Van boom,
R.Kaptein.
|
|
|
Ref.
|
|
J Mol Biol, 1987,
193,
213-216.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #9
|
|
|
Title
|
|
Restrained molecular dynamics procedure for protein tertiary structure determination from nmr data: a lac repressor headpiece structure based on information on j-Coupling and from presence and absence of noes
|
|
|
Authors
|
|
J.De vlieg,
R.Boelens,
R.M.Scheek,
R.Kaptein,
W.F.Van gunsteren.
|
|
|
Ref.
|
|
isr j chem, 1986,
27,
181.
|
|
|
|
|
|
|
|
