2NZU

Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors G6P and FBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

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This is version 1.3 of the entry. See complete history


Literature

Structural Mechanism for the Fine-tuning of CcpA Function by The Small Molecule Effectors Glucose 6-Phosphate and Fructose 1,6-Bisphosphate.

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

(2007) J Mol Biol 368: 1042-1050

  • DOI: 10.1016/j.jmb.2007.02.054
  • Primary Citation of Related Structures:  
    2NZU, 2NZV, 2OEN

  • PubMed Abstract: 
  • In Gram-positive bacteria, carbon catabolite regulation (CCR) is mediated by the carbon catabolite control protein A (CcpA), a member of the LacI-GalR family of transcription regulators. Unlike other LacI-GalR proteins, CcpA is activated to bind DNA by binding the phosphoproteins HPr-Ser46-P or Crh-Ser46-P ...

    In Gram-positive bacteria, carbon catabolite regulation (CCR) is mediated by the carbon catabolite control protein A (CcpA), a member of the LacI-GalR family of transcription regulators. Unlike other LacI-GalR proteins, CcpA is activated to bind DNA by binding the phosphoproteins HPr-Ser46-P or Crh-Ser46-P. However, fine regulation of CCR is accomplished by the small molecule effectors, glucose 6-phosphate (G6P) and fructose 1,6-bisphosphate (FBP), which somehow enhance CcpA-(HPr-Ser46-P) binding to DNA. Unlike the CcpA-(HPr-Ser46-P) complex, DNA binding by CcpA-(Crh-Ser46-P) is not stimulated by G6P or FBP. To understand the fine-tuning mechanism of these effectors, we solved the structures of the CcpA core, DeltaCcpA, which lacks the N-terminal DNA-binding domain, in complex with HPr-Ser46-P and G6P or FBP. G6P and FBP bind in a deep cleft, between the N and C subdomains of CcpA. Neither interacts with HPr-Ser46-P. This suggests that one role of the adjunct corepressors is to buttress the DNA-binding conformation effected by the binding of HPr-Ser46-P to the CcpA dimer N subdomains. However, the structures reveal that an unexpected function of adjunct corepressor binding is to bolster cross interactions between HPr-Ser46-P residue Arg17 and residues Asp69 and Asp99 of the other CcpA subunit. These cross contacts, which are weak or not present in the CcpA-(Crh-Ser46-P) complex, stimulate the CcpA-(HPr-Ser46-P)-DNA interaction specifically. Thus, stabilization of the closed conformation and bolstering of cross contacts between CcpA and its other corepressor, HPr-Ser46-P, provide a molecular explanation for how adjunct corepressors G6P and FBP enhance the interaction between CcpA-(HPr-Ser46-P) and cognate DNA.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Unit 1000, University of Texas, MD Anderson Cancer Center University, 1515 Holcombe Boulevard, Houston, TX 77030, USA. maschuma@mdanderson.org



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catabolite control proteinA [auth G]280Priestia megateriumMutation(s): 0 
Gene Names: ccpA
UniProt
Find proteins for P46828 (Priestia megaterium)
Explore P46828 
Go to UniProtKB:  P46828
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46828
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphocarrier protein HPrB [auth L]88Priestia megateriumMutation(s): 1 
Gene Names: ptsH
UniProt
Find proteins for O69250 (Priestia megaterium)
Explore O69250 
Go to UniProtKB:  O69250
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69250
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B [auth L]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.63α = 90
b = 68.63β = 90
c = 230.251γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary