3ERE

Crystal structure of the arginine repressor protein from Mycobacterium tuberculosis in complex with the DNA operator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the arginine repressor protein in complex with the DNA operator from Mycobacterium tuberculosis.

Cherney, L.T.Cherney, M.M.Garen, C.R.Lu, G.J.James, M.N.

(2008) J.Mol.Biol. 384: 1330-1340

  • DOI: 10.1016/j.jmb.2008.10.015

  • PubMed Abstract: 
  • The arginine repressor (ArgR) from Mycobacterium tuberculosis (Mtb) is a gene product encoded by the open reading frame Rv1657. It regulates the L-arginine concentration in cells by interacting with ARG boxes in the promoter regions of the arginine b ...

    The arginine repressor (ArgR) from Mycobacterium tuberculosis (Mtb) is a gene product encoded by the open reading frame Rv1657. It regulates the L-arginine concentration in cells by interacting with ARG boxes in the promoter regions of the arginine biosynthesis and catabolism operons. Here we present a 2.5-A structure of MtbArgR in complex with a 16-bp DNA operator in the absence of arginine. A biological trimer of the protein-DNA complex is formed via the crystallographic 3-fold symmetry axis. The N-terminal domain of MtbArgR has a winged helix-turn-helix motif that binds to the major groove of the DNA. This structure shows that, in the absence of arginine, the ArgR trimer can bind three ARG box half-sites. It also reveals the structure of the whole MtbArgR molecule itself containing both N-terminal and C-terminal domains.


    Organizational Affiliation

    Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, 431 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginine repressor
D
170Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: argR (ahrC)
Find proteins for P9WPY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WPY9
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*DCP*DAP*DA)-3'A16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*DCP*DAP*DA)-3'B16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.128α = 90.00
b = 94.128β = 90.00
c = 147.014γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
ADSCdata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance