4E1P

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

PDB DOI: 10.2210/pdb4E1P/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.185
R-Value Work: 0.160
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.pone.0038542
Primary Citation of Related Structures:
4E1P, 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.

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein lsr2	A, B	61	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: lsr2, MT3704, MTCY07H7B.25, Rv3597c
UniProt
Find proteins for P9WIP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIP7 Go to UniProtKB: P9WIP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIP7
Protein Feature View Expand
Reference Sequence