1JE8

Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dimerization allows DNA target site recognition by the NarL response regulator.

Maris, A.E.Sawaya, M.R.Kaczor-Grzeskowiak, M.Jarvis, M.R.Bearson, S.M.Kopka, M.L.Schroder, I.Gunsalus, R.P.Dickerson, R.E.

(2002) Nat Struct Biol 9: 771-778

  • DOI: 10.1038/nsb845
  • Primary Citation of Related Structures:  
    1JE8

  • PubMed Abstract: 
  • Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component ...

    Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component response regulators can bind DNA. DNA recognition is accompanied by the formation of a new dimerization interface, which could occur only in the full-length protein via a large intramolecular domain rearrangement. The DNA is recognized by the concerted effects of solvation, van der Waals forces and inherent DNA deformability, rather than determined primarily by major groove hydrogen bonding. These subtle forces permit a small DNA-binding domain to perturb the DNA helix, leading to major DNA curvature and a transition from B- to A-form DNA at the binding site, where valine on the recognition helix interacts unexpectedly with the polar major groove floor.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, P.O. Box 951569, Los Angeles, California 90095-1569, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrate/Nitrite Response Regulator Protein NARLABEF82Escherichia coliMutation(s): 3 
Find proteins for P0AF28 (Escherichia coli (strain K12))
Explore P0AF28 
Go to UniProtKB:  P0AF28
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'C, D, G, H20N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download CCD File 
    A, B, E, F
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MSE
    Query on MSE
    A,B,E,FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
    External Ligand Annotations 
    IDBinding Affinity (Sequence Identity %)
    DNAKd :  0.15000000596046448   nM  PDBBind
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.12 Å
    • R-Value Free: 0.273 
    • R-Value Work: 0.228 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 76.257α = 90
    b = 52.741β = 90
    c = 83.863γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    TRUNCATEdata reduction
    GLRFphasing
    CNSrefinement
    CCP4data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2002-09-27
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance