Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.42 kDa 
• Atom Count: 894 
• Modelled Residue Count: 73 
• Deposited Residue Count: 73 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1LCD

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

• PDB DOI: 10.2210/pdb1LCD/pdb
• NDB: 1LCD

• Classification: GENE REGULATION/DNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1993-03-25 Released: 1994-01-31 
• Deposition Author(s): Chuprina, V.P., Rullmann, J.A.C., Lamerichs, R.M.J.N., Van Boom, J.H., Boelens, R., Kaptein, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 3 

Literature

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.

Chuprina, V.P., Rullmann, J.A., Lamerichs, R.M., van Boom, J.H., Boelens, R., Kaptein, R.

(1993) J Mol Biol 234: 446-462

• PubMed: 8230225 
• DOI: 10.1006/jmbi.1993.1598
• Primary Citation of Related Structures:  
  1LCC, 1LCD


• PubMed 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.

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Related Citations: 

• Assignment of the 1H-NMR Spectrum of a Lac Repressor Headpiece-Operator Complex in H2O and Identification of Noes. Consequences for Protein-DNA Interaction
  Lamerichs, R.M.J.N., Boelens, R., Van Der Marel, G.A., Van Boom, J.H., Kaptein, R.
  (1990) Eur J Biochem 194: 629

• Two-Dimensional NMR Study of a Protein-DNA Complex. Lac Repressor Headpiece-Operator Interaction
  Kaptein, R., Lamerichs, R.M.J.N., Boelens, R., Rullmann, J.A.C.
  (1990) Biochem Pharmacol 40: 89

• 1H NMR Study of a Complex between the Lac Repressor Headpiece and a 22 Base Pair Symmetric Lac Operator
  Lamerichs, R.M.J.N., Boelens, R., Van Der Marel, G.A., Van Boom, J.H., Kaptein, R., Buck, F., Fera, B., Rueterjans, H.
  (1989) Biochemistry 28: 2985

• NMR Based Docking Studies of Lac Repressor Headpiece on a Lac Operator Fragment
  Rullmann, J.A.C., Boelens, R., Kaptein, R.
  (1989) Ucla Symp Mol Cell Biol , New Ser 95: 11

• The Interaction of Lac Repressor Headpiece with its Operator: An NMR View
  Boelens, R., Lamerichs, R.M.J.N., Rullmann, J.A.C., Van Boom, J.H., Kaptein, R.
  (1988) Protein Seq Data Anal 1: 487

• 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
  De Vlieg, J., Scheek, R.M., Van Gunsteren, W.F., Berendsen, H.J.C., Kaptein, R., Thomason, J.
  (1988) Proteins 3: 209

• A Two-Dimensional NMR Study of the Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment
  Boelens, R., Scheek, R.M., Lamerichs, R.M.J.N., De Vlieg, J., Van Boom, J.H., Kaptein, R.
  (1987) Nato Asi Ser ,ser A 137: 191

• Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment Studied by Two-Dimensional Nuclear Magnetic Resonance
  Boelens, R., Scheek, R.M., Van Boom, J.H., Kaptein, R.
  (1987) J Mol Biol 193: 213

• 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
  De Vlieg, J., Boelens, R., Scheek, R.M., Kaptein, R., Van Gunsteren, W.F.
  (1986) Isr J Chem 27: 181

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Organizational Affiliation: 

Bijvoet Center for Biomolecular Research, University of Utrecht, The Netherlands.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lac Repressor	C [auth A]	51	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P03023 (Escherichia coli (strain K12)) Explore P03023  Go to UniProtKB:  P03023

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*G)-3')	A [auth B]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')	B [auth C]	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 3 
• OLDERADO: 1LCD Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-03-25 
• Released Date: 1994-01-31 
Deposition Author(s): Chuprina, V.P., Rullmann, J.A.C., Lamerichs, R.M.J.N., Van Boom, J.H., Boelens, R., Kaptein, R.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations, Other