Macromolecule Content

• Total Structure Weight: 27.76 kDa 
• Atom Count: 1891 
• Residue Count: 170 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1L1M

SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1

• DOI: 10.2210/pdb1L1M/pdb
• BMRB: 5345
• NDB: 1L1M

• Classification: TRANSCRIPTION REGULATOR/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-02-19 Released: 2002-06-26 
• Deposition Author(s): Kalodimos, C.G., Bonvin, A.M.J.J., Salinas, R.K., Wechselberger, R., Boelens, R., Kaptein, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.

Kalodimos, C.G., Bonvin, A.M., Salinas, R.K., Wechselberger, R., Boelens, R., Kaptein, R.

(2002) EMBO J 21: 2866-2876

• PubMed: 12065400 
• DOI: 10.1093/emboj/cdf318
• Primary Citation of Related Structures:  
  1L1M


• PubMed Abstract: 
  

The lac repressor-operator system is a model system for understanding protein-DNA interactions and allosteric mechanisms in gene regulation. Despite the wealth of biochemical data provided by extensive mutations of both repressor and operator, the specific recognition mechanism of the natural lac operators by lac repressor has remained elusive. Here we present the first high-resolution structure of a dimer of the DNA-binding domain of lac repressor bound to its natural operator 01. The global positioning of the dimer on the operator is dramatically asymmetric, which results in a different pattern of specific contacts between the two sites. Specific recognition is accomplished by a combination of elongation and twist by 48 degrees of the right lac subunit relative to the left one, significant rearrangement of many side chains as well as sequence-dependent deformability of the DNA. The set of recognition mechanisms involved in the lac repressor-operator system is unique among other protein-DNA complexes and presents a nice example of the adaptability that both proteins and DNA exhibit in the context of their mutual interaction.

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Related Citations: 

• Strong DNA binding by covalently linked dimeric lac headpiece: evidence for the crucial role of the hinge helices
  Kalodimos, C.G., Folkers, G., Boelens, R., Kaptein, R.
  (2001) Proc Natl Acad Sci U S A 98: 6039

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Organizational Affiliation: 

Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose operon repressor	A, B	62	Escherichia coli	Mutation(s): 1  Gene Names: lacI
Find proteins for P03023 (Escherichia coli (strain K12)) Explore P03023  Go to UniProtKB:  P03023

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3'	C	23	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'	D	23	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1L1M Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-19 
• Released Date: 2002-06-26 
Deposition Author(s): Kalodimos, C.G., Bonvin, A.M.J.J., Salinas, R.K., Wechselberger, R., Boelens, R., Kaptein, R.

Revision History 

• Version 1.0: 2002-06-26
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance