1RZR

crystal structure of transcriptional regulator-phosphoprotein-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P.

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

(2004) Cell 118: 731-741

  • DOI: 10.1016/j.cell.2004.08.027
  • Primary Citation of Related Structures:  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 regu ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Glucose-resistance amylase regulator
G, C, A
332Bacillus megateriumGene Names: ccpA
Find proteins for P46828 (Bacillus megaterium)
Go to UniProtKB:  P46828
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Glucose-resistance amylase regulator
D
332Bacillus megateriumGene Names: ccpA
Find proteins for P46828 (Bacillus megaterium)
Go to UniProtKB:  P46828
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Phosphocarrier protein HPr
T, L, Y, S
88Bacillus megateriumGene Names: ptsH
EC: 2.7.11.-
Find proteins for O69250 (Bacillus megaterium)
Go to UniProtKB:  O69250
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'H,E16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'R,B16N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
L, S, T, Y
L-PEPTIDE LINKINGC3 H8 N O6 PSER
MSE
Query on MSE
A, C, D, G
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 105.710α = 90.00
b = 109.240β = 90.05
c = 117.810γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNSphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance