6QKQ | pdb_00006qkq

NMR solution structure of LSR2-T112D binding domain.

• PDB DOI: https://doi.org/10.2210/pdb6QKQ/pdb
• BMRB: 34359

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-30 Released: 2019-07-17 
• Deposition Author(s): Barthe, P., Cohen-Gonsaud, M., Mukamolova, G.V.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112.

Alqaseer, K., Turapov, O., Barthe, P., Jagatia, H., De Visch, A., Roumestand, C., Wegrzyn, M., Bartek, I.L., Voskuil, M.I., O'Hare, H.M., Ajuh, P., Bottrill, A.R., Witney, A.A., Cohen-Gonsaud, M., Waddell, S.J., Mukamolova, G.V.

(2019) Mol Microbiol 112: 1847-1862

• PubMed: 31562654 
• DOI: https://doi.org/10.1111/mmi.14398
• Primary Citation Related Structures: 
  6QKP, 6QKQ


• PubMed Abstract: 
  

  Mycobacterium tuberculosis (Mtb) is able to persist in the body through months of multi-drug therapy. Mycobacteria possess a wide range of regulatory proteins, including the protein kinase B (PknB) which controls peptidoglycan biosynthesis during growth. Here, we observed that depletion of PknB resulted in specific transcriptional changes that are likely caused by reduced phosphorylation of the H-NS-like regulator Lsr2 at threonine 112. The activity of PknB towards this phosphosite was confirmed with purified proteins, and this site was required for adaptation of Mtb to hypoxic conditions, and growth on solid media. Like H-NS, Lsr2 binds DNA in sequence-dependent and non-specific modes. PknB phosphorylation of Lsr2 reduced DNA binding, measured by fluorescence anisotropy and electrophoretic mobility shift assays, and our NMR structure of phosphomimetic T112D Lsr2 suggests that this may be due to increased dynamics of the DNA-binding domain. Conversely, the phosphoablative T112A Lsr2 had increased binding to certain DNA sites in ChIP-sequencing, and Mtb containing this variant showed transcriptional changes that correspond with the change in DNA binding. In summary, PknB controls Mtb growth and adaptations to the changing host environment by phosphorylating the global transcriptional regulator Lsr2.

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Organizational Affiliation: 
• Leicester Tuberculosis Research Group, Department of Respiratory Sciences, University of Leicester, Leicester, LE2 9HN, UK.
Department of Basic Science, Faculty of Nursing, University of Kufa, Najaf Governorate, P.O. Box 21, Kufa, Najaf, Iraq.
Centre de Biochimie Structurale, CNRS, INSERM, University of Montpellier, 34090, Montpellier, France.
Wellcome Trust Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK.
Core Biotechnology Services, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
LISCB, Department of Molecular and Cell Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Gemini Biosciences Ltd, Liverpool Science Park, Liverpool, L7 8TX, UK.
Protein Nucleic Acid Laboratory, University of Leicester, Leicester, LE1 7RH, UK.
Institute for Infection and Immunity, St George's University of London, London, SW17 0RE, UK.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 5.51 kDa 
• Atom Count: 366 
• Modeled Residue Count: 48 
• Deposited Residue Count: 51 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoid-associated protein Lsr2	A	51	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: lsr2, Rv3597c, MTCY07H7B.25
UniProt
Find proteins for P9WIP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIP7  Go to UniProtKB:  P9WIP7

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Barthe, P., Cohen-Gonsaud, M., Mukamolova, G.V.

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Database references
• Version 1.3: 2023-06-14
  Changes: Database references, Other
• Version 1.4: 2024-06-19
  Changes: Data collection, Database references