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: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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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
  • Primary Citation of Related Structures:  
    3ERE

  • 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 biosynthesis and catabolism operons ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginine repressorA [auth D]170Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: argRahrCRv1657MT1695MTCY06H11.22
UniProt
Find proteins for P9WPY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPY9 
Go to UniProtKB:  P9WPY9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*DCP*DAP*DA)-3'B [auth A]16N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*DCP*DAP*DA)-3'C [auth B]16N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download Ideal Coordinates CCD File 
      D, E [auth D], F [auth D]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.50 Å
      • R-Value Free: 0.255 
      • R-Value Work: 0.227 
      • R-Value Observed: 0.227 
      • Space Group: P 63 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 94.128α = 90
      b = 94.128β = 90
      c = 147.014γ = 120
      Software Package:
      Software NamePurpose
      ADSCdata collection
      MOLREPphasing
      CNSrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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