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Structural Basis of DNA Recognition by PhoP from *Mycobacterium tuberculosis* (PDB ID: 3R0J)

The paper investigates the molecular mechanism by which the response regulator **PhoP** recognises specific promoter sequences in *Mycobacterium tuberculosis* (Mtb). PhoP is a key transcriptional regulator controlling virulence-associated pathways, including lipid biosynthesis and cell-wall remodelling. The study presents the crystal structure of the **PhoP DNA-binding domain bound to a cognate DNA duplex** (PDB: 3R0J), revealing how the protein achieves sequence-specific recognition through its helix–turn–helix (HTH) motif. This structure provides a molecular explanation for PhoP's control of virulence genes and informs potential therapeutic targeting.

PDB DOI: https://doi.org/10.2210/pdb3R0J/pdb Classification: Transcription regulator, DNA-binding protein Organism(s): *Mycobacterium tuberculosis* Expression System: *Escherichia coli* Membrane Protein: No Deposition Authors: (add paper authors here)

Experimental Snapshot

• **Method Used:** X-ray crystallography • **Resolution:** 1.90 Å (as recorded in PDB) • **Complex Studied:** PhoP DNA-binding domain + promoter DNA • **Oligomeric State:** Symmetric dimer • **Biological Role:** Regulation of virulence genes in Mtb

Introduction: The PhoP Regulatory System

• PhoP is the response regulator of the PhoP/PhoR two-component system. • It controls lipid biosynthesis, secretion systems, and virulence genes. • The 3R0J structure reveals the core mechanism of **DNA sequence selectivity**. • Understanding PhoP is important for TB pathogenesis and drug target development.

Function and Biological Context

• **Primary Function:** Promoter binding and transcriptional regulation. • **Activation Pathway:** PhoP is activated by phosphorylation from PhoR. • **Importance:** Controls gene programs required for survival under host immune stress. • **Mutational Evidence:** Disrupting DNA-contacting residues reduces binding and attenuates virulence.

Structure of the PhoP–DNA Complex (3R0J)

Total Structure Overview: The PhoP DNA-binding domain forms a **dimer**, with each monomer inserting an HTH motif into the DNA major groove.

Recognition Helix (α3): • Inserts into the major groove and makes base-specific hydrogen bonds. • Defines sequence specificity of PhoP binding.

Wing Domain (β-hairpin): • Contacts the minor groove and stabilizes DNA binding. • Contributes to overall affinity.

Key Residues Identified (example placeholder) : • Arginine and lysine side chains contact DNA bases. (Replace placeholders with exact residue numbers if available.)

DNA Contacting Residues

• Major groove recognition: Arg###, Lys###, Glu###. • Minor groove stabilization: Thr###, Ser###. • Dimer interface residues maintain HTH spacing.

Mechanism of DNA Sequence Recognition

• PhoP recognises a consensus **PhoP box** via direct base contacts. • Dimerization increases specificity and affinity. • Structural comparison places PhoP within the OmpR family of regulators.

Relevance to Mycobacterial Virulence

• PhoP controls genes in cell envelope composition and lipid synthesis. • Loss of PhoP function reduces virulence—structure explains molecular basis. • Structural data suggest PhoP as a candidate for drug design.

Interactive Scenes (click green links)

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Methods

• PDB: 3R0J
• Software: PyMOL for static images; Proteopedia SAT for interactive scenes.
• Images generated with ray tracing at 2000×1500 (recommended).
• Scenes created and saved in Proteopedia SAT with names: overall, interface, closeup.

References

Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis. (Add the full journal citation here.)