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 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.6 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: https://doi.org/10.1074/jbc.M509977200
  • Primary Citation of Related Structures:  
    1ZVV

  • 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. 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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-resistance amylase regulatorD [auth A],
F [auth B],
H [auth G]
332Bacillus subtilisMutation(s): 0 
Gene Names: ccpA
UniProt
Find proteins for P25144 (Bacillus subtilis (strain 168))
Explore P25144 
Go to UniProtKB:  P25144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25144
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HPr-like protein crhE [auth W],
G [auth P],
I [auth J]
85Bacillus subtilisMutation(s): 0 
Gene Names: crh
UniProt
Find proteins for O06976 (Bacillus subtilis (strain 168))
Explore O06976 
Go to UniProtKB:  O06976
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06976
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA recognition strand CREA [auth O],
B [auth T],
C [auth R]
16synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
J [auth O]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth O],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth P],
S [auth G],
T [auth G]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
E [auth W],
G [auth P],
I [auth J]
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 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.69α = 90
b = 158.1β = 100.73
c = 125.47γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-07
    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: 2012-08-22
    Changes: Other
  • Version 1.4: 2017-01-11
    Changes: Other
  • Version 1.5: 2023-02-22
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.6: 2023-09-20
    Changes: Data collection, Refinement description