6O6N | pdb_00006o6n

Structure of the regulator FasR from Mycobacterium tuberculosis in complex with C20-CoA

• PDB DOI: https://doi.org/10.2210/pdb6O6N/pdb

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


• Deposited: 2019-03-07 Released: 2020-03-11 
• Deposition Author(s): Larrieux, N., Trajtenberg, F., Lara, J., Gramajo, H., Buschiazzo, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Mycobacterium tuberculosis FasR senses long fatty acyl-CoA through a tunnel and a hydrophobic transmission spine.

Lara, J., Diacovich, L., Trajtenberg, F., Larrieux, N., Malchiodi, E.L., Fernandez, M.M., Gago, G., Gramajo, H., Buschiazzo, A.

(2020) Nat Commun 11: 3703-3703

• PubMed: 32710080 
• DOI: https://doi.org/10.1038/s41467-020-17504-x
• Primary Citation Related Structures: 
  6O6N, 6O6O, 6O6P


• PubMed Abstract: 
  

  Mycobacterium tuberculosis is a pathogen with a unique cell envelope including very long fatty acids, implicated in bacterial resistance and host immune modulation. FasR is a TetR-like transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis. Here we disclose crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its molecular sensory and switching mechanisms. A long tunnel traverses the entire effector-binding domain, enabling long fatty acyl effectors to bind. Only when the tunnel is entirely occupied, the protein dimer adopts a rigid configuration with its DNA-binding domains in an open state, leading to DNA dissociation. The protein-folding hydrophobic core connects the two domains, and is completed into a continuous spine when the effector binds. Such a transmission spine is conserved in a large number of TetR-like regulators, offering insight into effector-triggered allosteric functional control.

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Organizational Affiliation: 
• Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina.
Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Rosario, 2000, Argentina.
Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay.
Instituto de Estudios de la Inmunidad Humoral (IDEHU/CONICET-UBA), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, 1113, Argentina.
Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina. [e-mail].
Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay. [e-mail].
Integrative Microbiology of Zoonotic Agents, International Joint Research Unit, Department of Microbiology, Institut Pasteur, Paris, 75724, Cedex 15, France. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.73 kDa 
• Atom Count: 1,792 
• Modeled Residue Count: 195 
• Deposited Residue Count: 195 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator	A	195	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  kstR2_2, kstR2_1, kstR2_3, kstR2_4, kstR2_5, kstR2_6, kstR2_7, DSI35_30495, ERS007661_03222, ERS007663_03464, ERS007665_00400, ERS007720_01056, ERS007741_00500, ERS023446_00266, ERS027646_02562, ERS027651_00856, ERS027652_02035, ERS027653_03199, ERS027656_00595, ERS027666_01457, ERS124361_00903, SAMEA2682864_03848, SAMEA2683035_03897
UniProt
Find proteins for O05858 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O05858  Go to UniProtKB:  O05858

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5F9 (Subject of Investigation/LOI)	B [auth A]	Arachinoyl-CoA C41 H74 N7 O17 P3 S JYLSVNBJLYCSSW-DLATUHJOSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.210 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/647

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.146	α = 90
b = 108.146	β = 90
c = 43.562	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
TRUNCATE	data reduction
Arcimboldo	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Larrieux, N., Trajtenberg, F., Lara, J., Gramajo, H., Buschiazzo, A.

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references