1ZVV

Crystal structure of a ccpa-crh-dna complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation.

Schumacher, M.A.Seidel, G.Hillen, W.Brennan, R.G.

(2006) J.Biol.Chem. 281: 6793-6800

  • DOI: 10.1074/jbc.M509977200

  • PubMed Abstract: 
  • In Gram-positive bacteria, the catabolite control protein A (CcpA) functions as the master transcriptional regulator of carbon catabolite repression/regulation (CCR). To effect CCR, CcpA binds a phosphoprotein, either HPr-Ser46-P or Crh-Ser46-P. Alth ...

    In Gram-positive bacteria, the catabolite control protein A (CcpA) functions as the master transcriptional regulator of carbon catabolite repression/regulation (CCR). To effect CCR, CcpA binds a phosphoprotein, either HPr-Ser46-P or Crh-Ser46-P. Although Crh and histidine-containing protein (HPr) are structurally homologous, CcpA binds Crh-Ser46-P more weakly than HPr-Ser46-P. Moreover, Crh can form domain-swapped dimers, which have been hypothesized to be functionally relevant in CCR. To understand the molecular mechanism of Crh-Ser46-P regulation of CCR, we determined the structure of a CcpA-(Crh-Ser46-P)-DNA complex. The structure reveals that Crh-Ser46-P does not bind CcpA as a dimer but rather interacts with CcpA as a monomer in a manner similar to that of HPr-Ser46-P. The reduced affinity of Crh-Ser46-P for CcpA as compared with that of HPr-Ser46 P is explained by weaker Crh-Ser46-P interactions in its contact region I to CcpA, which causes this region to shift away from CcpA. Nonetheless, the interface between CcpA and helix alpha 2 of the second contact region (contact region II) of Crh-Ser46-P is maintained. This latter finding demonstrates that this contact region is necessary and sufficient to throw the allosteric switch to activate cre binding by CcpA.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glucose-resistance amylase regulator
A, B, G
332Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ccpA (alsA, amyR, graR)
Find proteins for P25144 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P25144
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HPr-like protein crh
W, P, J
85Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: crh (yvcM)
Find proteins for O06976 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O06976
Entity ID: 1
MoleculeChainsLengthOrganism
DNA recognition strand CREO,T,R16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, G, O, P
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
J, P, W
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.690α = 90.00
b = 158.100β = 100.73
c = 125.470γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling
CNSrefinement
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-08-22
    Type: Other
  • Version 1.4: 2017-01-11
    Type: Other