3OQM

structure of ccpa-hpr-ser46p-ackA2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.

Schumacher, M.A.Sprehe, M.Bartholomae, M.Hillen, W.Brennan, R.G.

(2011) Nucleic Acids Res. 39: 2931-2942

  • DOI: 10.1093/nar/gkq1177
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR proteins, CcpA is activated for DNA binding by fir ...

    In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR proteins, CcpA is activated for DNA binding by first forming a complex with the phosphoprotein HPr-Ser46-P. Bacillus subtilis CcpA functions as both a transcription repressor and activator and binds to more than 50 operators called catabolite response elements (cres). These sites are highly degenerate with the consensus, WTGNNARCGNWWWCAW. How CcpA-(HPr-Ser46-P) binds such diverse sequences is unclear. To gain insight into this question, we solved the structures of the CcpA-(HPr-Ser46-P) complex bound to three different operators, the synthetic (syn) cre, ackA2 cre and gntR-down cre. Strikingly, the structures show that the CcpA-bound operators display different bend angles, ranging from 31° to 56°. These differences are accommodated by a flexible linkage between the CcpA helix-turn-helix-loop-helix motif and hinge helices, which allows independent docking of these DNA-binding modules. This flexibility coupled with an abundance of non-polar residues capable of non-specific nucleobase interactions permits CcpA-(HPr-Ser46-P) to bind diverse operators. Indeed, biochemical data show that CcpA-(HPr-Ser46-P) binds the three cre sites with similar affinities. Thus, the data reveal properties that license this protein to function as a global transcription regulator.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. maschuma@mdanderson.org




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catabolite control protein A
A, C
339Bacillus 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: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphocarrier protein HPr
S, D
87Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ptsH
Find proteins for P08877 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P08877
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*TP*GP*TP*AP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*A)-3'E16Bacillus subtilis
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*TP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*TP*AP*CP*AP*A)-3'B16Bacillus subtilis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
D, S
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.240α = 90.00
b = 103.540β = 90.00
c = 176.650γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSrefinement
MOLREPphasing
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance