4IHW

Crystal structure of Fis bound to 27 bp Inosine substituted DNA F28-dI (AAATTTGTTTGAICITTGAGCAAATTT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.

Hancock, S.P.Ghane, T.Cascio, D.Rohs, R.Di Felice, R.Johnson, R.C.

(2013) Nucleic Acids Res 41: 6750-6760

  • DOI: https://doi.org/10.1093/nar/gkt357
  • Primary Citation of Related Structures:  
    4IHV, 4IHW, 4IHX, 4IHY

  • PubMed Abstract: 

    The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes.


  • Organizational Affiliation

    Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095-1737, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding protein fis
A, B
98Escherichia coli K-12Mutation(s): 0 
Gene Names: ECDH1ME8569_3147EcDH1_0445fis
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
27-bp DNA Strand A27N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
27-bp DNA Strand B27N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.37α = 90
b = 94.4β = 90
c = 154.99γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2013-07-31
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description