2WGB | pdb_00002wgb

Crystal structure of the TetR-like transcriptional regulator LfrR from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb2WGB/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycolicibacterium smegmatis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-04-16 Released: 2009-10-20 
• Deposition Author(s): Bellinzoni, M., Buroni, S., Riccardi, G., De Rossi, E., Alzari, P.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Structural Plasticity and Distinct Drug-Binding Modes of Lfrr, a Mycobacterial Efflux Pump Regulator.

Bellinzoni, M., Buroni, S., Schaeffer, F., Riccardi, G., De Rossi, E., Alzari, P.M.

(2009) J Bacteriol 191: 7531

• PubMed: 19820093 
• DOI: https://doi.org/10.1128/JB.00631-09
• Primary Citation Related Structures: 
  2V57, 2WGB


• PubMed Abstract: 
  

  The TetR-like transcriptional repressor LfrR controls the expression of the gene encoding the Mycobacterium smegmatis efflux pump LfrA, which actively extrudes fluoroquinolones, cationic dyes, and anthracyclines from the cell and promotes intrinsic antibiotic resistance. The crystal structure of the apoprotein form of the repressor reveals a structurally asymmetric homodimer exhibiting local unfolding and a blocked drug-binding site, emphasizing the significant conformational plasticity of the protein necessary for DNA and multidrug recognition. Crystallographic and calorimetric studies of LfrR-drug complexes further confirm the intrinsic flexibility of the homodimer, which provides a dynamic mechanism to broaden multidrug binding specificity and may be a general property of transcriptional repressors regulating microbial efflux pump expression.

---

Organizational Affiliation: 
• Institut Pasteur, Unité de Biochimie Structurale and CNRS URA 2185, Institut Pasteur, 75724 Paris Cedex 15, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.78 kDa 
• Atom Count: 2,699 
• Modeled Residue Count: 325 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR	A, B	190	Mycolicibacterium smegmatis	Mutation(s): 0
UniProt
Find proteins for Q58L87 (Mycolicibacterium smegmatis) Explore Q58L87  Go to UniProtKB:  Q58L87

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.646	α = 90
b = 86.646	β = 90
c = 96.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Bellinzoni, M., Buroni, S., Riccardi, G., De Rossi, E., Alzari, P.M.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other