1RZR

crystal structure of transcriptional regulator-phosphoprotein-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • R-Value Observed: 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:  
    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 ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-resistance amylase regulatorG [auth A],
F [auth C],
E [auth G]
332Priestia megateriumMutation(s): 10 
Gene Names: ccpA
UniProt
Find proteins for P46828 (Priestia megaterium)
Explore P46828 
Go to UniProtKB:  P46828
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UniProt GroupP46828
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-resistance amylase regulatorH [auth D]332Priestia megateriumMutation(s): 9 
Gene Names: ccpA
UniProt
Find proteins for P46828 (Priestia megaterium)
Explore P46828 
Go to UniProtKB:  P46828
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UniProt GroupP46828
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphocarrier protein HPrJ [auth L],
L [auth S],
I [auth T],
K [auth Y]
88Priestia megateriumMutation(s): 1 
Gene Names: ptsH
UniProt
Find proteins for O69250 (Priestia megaterium)
Explore O69250 
Go to UniProtKB:  O69250
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UniProt GroupO69250
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'C [auth E],
A [auth H]
16N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'D [auth B],
B [auth R]
16N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
E [auth G],
F [auth C],
G [auth A]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
SEP
Query on SEP
I [auth T],
J [auth L],
K [auth Y],
L [auth S]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.71α = 90
b = 109.24β = 90.05
c = 117.81γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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