9F80 | pdb_00009f80

Crystal structure of Rv2242 regulator C-terminal fragment (161-414)

• PDB DOI: https://doi.org/10.2210/pdb9F80/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-06 Released: 2024-12-18 
• Deposition Author(s): Megalizzi, V., Tanina, A., Grosse, C., Mirgaux, M., Legrand, P., Dias Mirandela, G., Wohlkonig, A., Bifani, P., Wintjens, R.
• Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.206 (DCC) 

Literature

Domain architecture of the Mycobacterium tuberculosis MabR ( Rv2242 ), a member of the PucR transcription factor family.

Megalizzi, V., Tanina, A., Grosse, C., Mirgaux, M., Legrand, P., Dias Mirandela, G., Wohlkonig, A., Bifani, P., Wintjens, R.

(2024) Heliyon 10: e40494-e40494

• PubMed: 39641026 
• DOI: https://doi.org/10.1016/j.heliyon.2024.e40494
• Primary Citation Related Structures: 
  9F80, 9FB1


• PubMed Abstract: 
  

  MabR ( Rv2242 ), a PucR-type transcription factor, plays a crucial role in regulating mycolic acid biosynthesis in Mycobacterium tuberculosis . To understand its regulatory mechanisms, we determined the crystal structures of its N-terminal and C-terminal domains. The N-terminal domain adopts a globin-like fold, while the C-terminal domain comprises an α/β GGDEF domain and an all-α effector domain with a helix-turn-helix DNA-binding motif. This unique domain combination is specific to Actinomycetes . Biochemical and computational studies suggest that full-length MabR forms both dimeric and tetrameric assemblies in solution. Structural analysis revealed two distinct dimerization interfaces within the N- and C-terminal domains, further supporting a tetrameric organization. These findings provide valuable insights into the domain architecture, oligomeric state, and potential regulatory mechanisms of MabR.

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Organizational Affiliation: 
• Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium.
Laboratoire de Chimie Biologique Structurale (CBS), Unité de Chimie Physique Théorique et Structurale (UCPTS), Department of Chemistry, Faculty of Sciences, University of Namur, Belgium.
Center of Microscopy and Molecular Imaging (CMMI), Biopark Charleroi, Université Libre de Bruxelles, Gosselies, Belgium.
SOLEIL synchrotron, Gif-sur-Yvette, France.
Biology of Membrane Transport Laboratory, Molecular Biology Department, Faculty of Sciences, Université Libre de Bruxelles, Belgium.
Center for Structural Biology, Vlaams Institute voor Biotechnology (VIB), Brussels, Belgium.
A∗STAR Infectious Diseases Laboratory, Agency for Science, Technology and Research (A∗STAR), Singapore.
Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.25 kDa 
• Atom Count: 1,834 
• Modeled Residue Count: 243 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Rv2242	A	275	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv2242, MTCY427.23
UniProt
Find proteins for P9WPH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPH5  Go to UniProtKB:  P9WPH5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.206 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.04	α = 90
b = 75.28	β = 90
c = 139.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHELXD	phasing
PHASER	phasing
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Megalizzi, V., Tanina, A., Grosse, C., Mirgaux, M., Legrand, P., Dias Mirandela, G., Wohlkonig, A., Bifani, P., Wintjens, R.

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Funding Organization	Location	Grant Number
Fonds National de la Recherche Scientifique (FNRS)	Belgium	CR40003580

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release