Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 13078.65 
• Atom Count: 834 
• Residue Count: 122 
• Unique protein chains: 1

4E1P

Crystal structure of the dimerization domain of Lsr2 from Mycobacterium tuberculosis in the P 1 21 1 space group

• DOI: 10.2210/pdb4E1P/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2012-03-06 Released: 2012-06-20 
• Deposition Author(s): Summers, E.L., Meindl, K., Uson, I., Arcus, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.728 Å
• R-Value Free: 0.185 
• R-Value Work: 0.160 

Literature

The structure of the oligomerization domain of Lsr2 from Mycobacterium tuberculosis reveals a mechanism for chromosome organization and protection.

Summers, E.L., Meindl, K., Uson, I., Mitra, A.K., Radjainia, M., Colangeli, R., Alland, D., Arcus, V.L.

(2012) Plos One 7: e38542-e38542

• PubMed: 22719899 
• DOI: 10.1371/journal.pone.0038542
• Primary Citation of Related Structures:  
  4E1R


• PubMed Abstract: 
  

Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNA-binding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal cross-linking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 Å resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß-ß-a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel β-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated.

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Organizational Affiliation: 

Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein lsr2	A, B	61	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mutation(s): 0  Gene Names: lsr2
Find proteins for P9WIP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WIP7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.728 Å
• R-Value Free: 0.185 
• R-Value Work: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 32.510	α = 90.00
b = 27.030	β = 94.31
c = 56.830	γ = 90.00

Software Package:

Software Name	Purpose
Arcimboldo	phasing
PDB_EXTRACT	data extraction
MAR345dtb	data collection
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-06 
• Released Date: 2012-06-20 
• Deposition Author(s): Summers, E.L., Meindl, K., Uson, I., Arcus, V.L.

Revision History 

• Version 1.0: 2012-06-20
  Type: Initial release
• Version 1.1: 2013-01-23
  Type: Database references