6A4L

AcrR from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb6A4L/pdb

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

Deposited: 2018-06-20 Released: 2019-06-26
Deposition Author(s): Kang, S.M.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.259
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of AcrR from Mycobacterium tuberculosis reveals a one-component transcriptional regulation mechanism.

Kang, S.M., Kim, D.H., Jin, C., Ahn, H.C., Lee, B.J.

(2019) FEBS Open Bio 9: 1713-1725

PubMed: 31369208 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/2211-5463.12710
Primary Citation of Related Structures:
6A4L, 6A4W

PubMed Abstract:
Transcriptional regulator proteins are closely involved in essential survival strategies in bacteria. AcrR is a one-component allosteric repressor of the genes associated with lipid transport and antibiotic resistance. When fatty acid ligands bind to the C-terminal ligand-binding cavity of AcrR, a conformational change in the N-terminal operator-binding region of AcrR is triggered, which releases the repressed DNA and initiates transcription. This paper focuses on the structural transition mechanism of AcrR of Mycobacterium tuberculosis upon DNA and ligand binding. AcrR loses its structural integrity upon ligand-mediated structural alteration and bends toward the promoter DNA in a more compact form, initiating a rotational motion. Our functional characterization of AcrR and description of the ligand- and DNA-recognition mechanism may facilitate the discovery of new therapies for tuberculosis.

Organizational Affiliation

The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 52.4 kDa
Atom Count: 3,211
Modelled Residue Count: 394
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator	A, B	230	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: acrR, ERS007657_03305, ERS007663_01106, ERS007670_02655, ERS007672_02023, ERS007679_02277, ERS007681_02293, ERS007688_01622, ERS007703_02625, ERS007722_01260... acrR, ERS007657_03305, ERS007663_01106, ERS007670_02655, ERS007672_02023, ERS007679_02277, ERS007681_02293, ERS007688_01622, ERS007703_02625, ERS007722_01260, ERS023446_03575, ERS027646_00827, ERS027651_03158, ERS027653_04028, ERS027654_02941, ERS027659_02538, ERS027661_02360, ERS031537_01877, ERS124361_02153, SAMEA2682864_00974, SAMEA2683035_01767
UniProt
Find proteins for O07229 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O07229 Go to UniProtKB: O07229
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O07229
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], G [auth B], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	E [auth A], F [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.259
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.752	α = 90
b = 118.752	β = 90
c = 93.456	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

Kang, S.M.

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2018R1A2A1A19018526

Revision History (Full details and data files)

Version 1.0: 2019-06-26
Type: Initial release
Version 1.1: 2020-04-29
Changes: Database references, Structure summary
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary