1ZG5

NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Primary and Secondary Modes of DNA Recognition by the NarL Two-Component Response Regulator.

Maris, A.E., Kaczor-Grzeskowiak, M., Ma, Z., Kopka, M.L., Gunsalus, R.P., Dickerson, R.E.

(2005) Biochemistry 44: 14538-14552

  • DOI: 10.1021/bi050734u
  • Primary Citation of Related Structures:  
    1ZG1, 1ZG5

  • PubMed Abstract: 

    • NarL is a model response regulator for bacterial two-component signal transduction. The NarL C-terminal domain DNA binding domain alone (NarL(C)) contains all essential DNA binding determinants of the full-length NarL transcription factor. In the full-length NarL protein, the N-terminal regulatory domain must be phosphorylated to release the DNA binding determinants; however, the first NarL(C)-DNA cocrystal structure showed that dimerization of NarL(C) on DNA occurs in a manner independent of the regulatory domain [Maris, A ...

    NarL is a model response regulator for bacterial two-component signal transduction. The NarL C-terminal domain DNA binding domain alone (NarL(C)) contains all essential DNA binding determinants of the full-length NarL transcription factor. In the full-length NarL protein, the N-terminal regulatory domain must be phosphorylated to release the DNA binding determinants; however, the first NarL(C)-DNA cocrystal structure showed that dimerization of NarL(C) on DNA occurs in a manner independent of the regulatory domain [Maris, A. E., et al. (2002) Nat. Struct. Biol. 9, 771-778]. Dimerization via the NarL(C) C-terminal helix conferred high-affinity recognition of the tail-to-tail promoter site arrangement. Here, two new cocrystal structures are presented of NarL(C) complexed with additional 20mer oligonucleotides representative of other high-affinity tail-to-tail NarL binding sites found in upstream promoter regions. DNA structural recognition properties are described, such as backbone flexibility and groove width, that facilitate NarL(C) dimerization and high-affinity recognition. Lys 188 on the recognition helix accommodates DNA sequence variation between the three different cocomplexes by providing flexible specificity, recognizing the DNA major groove floor directly and/or via bridging waters. The highly conserved Val 189, which enforced significant DNA base distortion in the first cocrystal structure, enforces similar distortions in the two new cocrystal structures. Recognition also is conserved for Lys 192, which hydrogen bonds to guanines at regions of high DNA helical writhe. DNA affinity measurements for model NarL binding sites, including those that did not cocrystallize, suggest a framework for explaining the diversity of heptamer site arrangement and orientation.

    Related Citations: 
    • 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.D., Kopka, M.L., Schroeder, I., Gunsalus, R.P., Dickerson, R.E.
      (2002) Nat Struct Biol 9: 771
    • Structure of the Escherichia coli response regulator NarL
      Baikalov, I., Schroeder, I., Kaczor-Grzeskowiak, M., Grzeskowiak, K., Gunsalus, R.P., Dickerson, R.E.
      (1996) Biochemistry 35: 11053
    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA. aemaris@lbl.gov



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrate/nitrite response regulator protein narLE [auth A],
F [auth B],
G [auth E],
H [auth F]		82Escherichia coliMutation(s): 3 
Gene Names: narL
UniProt
Find proteins for P0AF28 (Escherichia coli (strain K12))
Explore P0AF28 
Go to UniProtKB:  P0AF28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AF28
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3'A [auth C],
B [auth D],
C [auth G],
D [auth H]		20N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.89α = 90
b = 52.57β = 89.995
c = 84.61γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance