Structure of apo transcription regulator B. megaterium

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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This is version 1.4 of the entry. See complete history


Structural studies on the apo transcription factor form B. megaterium

Schumacher, M.A.Allen, G.S.Diel, M.Seidel, G.Hillen, W.Brennan, R.G.

(2004) Cell 118: 731-741

  • DOI: https://doi.org/10.1016/j.cell.2004.08.027
  • Primary Citation of Related Structures:  
    1RZR, 1SXG, 1SXH, 1SXI

  • PubMed Abstract: 

    Carbon catabolite repression (CCR) is one of the most fundamental environmental-sensing mechanisms in bacteria and imparts competitive advantage by establishing priorities in carbon metabolism. In gram-positive bacteria, the master transcription regulator of CCR is CcpA. CcpA is a LacI-GalR family member that employs, as an allosteric corepressor, the phosphoprotein HPr-Ser46-P, which is formed in glucose-replete conditions. Here we report structures of the Bacillus megaterium apoCcpA and a CcpA-(HPr-Ser46-P)-DNA complex. These structures reveal that HPr-Ser46-P mediates a novel two-component allosteric DNA binding activation mechanism that involves both rotation of the CcpA subdomains and relocation of pivot-point residue Thr61, which leads to juxtaposition of the DNA binding regions permitting "hinge" helix formation in the presence of cognate DNA. The structure of the CcpA-(HPr-Ser46-P)-cre complex also reveals the elegant mechanism by which CcpA family-specific interactions with HPr-Ser46-P residues Ser46-P and His15 partition the high-energy CCR and low-energy PTS pathways, the latter requiring HPr-His15-P.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland 97239, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-resistance amylase regulator280Priestia megateriumMutation(s): 8 
Gene Names: CCpa
Find proteins for P46828 (Priestia megaterium)
Explore P46828 
Go to UniProtKB:  P46828
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46828
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
B [auth D]
C [auth B]
D [auth I]
E [auth R]
B [auth D],
C [auth B],
D [auth I],
E [auth R],
F [auth T],
G [auth L],
H [auth K],
I [auth W],
J [auth G],
K [auth N],
L [auth M]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.24α = 90
b = 106.22β = 108.2
c = 157.74γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection