Crystal structure of E. coli YncE

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE

Kagawa, W.Sagawa, T.Niki, H.Kurumizaka, H.

(2011) Acta Crystallogr D Biol Crystallogr 67: 1045-1053

  • DOI: https://doi.org/10.1107/S0907444911045033
  • Primary Citation of Related Structures:  
    3VGZ, 3VH0

  • PubMed Abstract: 

    β-Propellers are widely utilized in nature as recognition modules. The well conserved β-propeller fold exhibits a high degree of functional diversity, which is probably accomplished through variations in the surface properties of the proteins. Little is known about the interactions between β-propeller proteins and nucleic acids. In the present study, it has been found that the bacterial β-propeller protein YncE binds to DNA. Crystal structures of YncE in the free form and complexed with DNA revealed that the surface region of YncE corresponding to the `canonical' substrate-binding site forms essential contacts with DNA. A single DNA base within a single-stranded DNA region is trapped in the hydrophobic pocket located within the central channel of the β-propeller protein. These data provide physical evidence for the DNA-binding ability of the previously uncharacterized YncE and also suggest that the `canonical' substrate-binding site may be commonly adapted to facilitate nucleic acid binding in a subset of β-propeller proteins.

  • Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YncE
A, B, C, D
353Escherichia coli K-12Mutation(s): 0 
Gene Names: yncE
Find proteins for P76116 (Escherichia coli (strain K12))
Explore P76116 
Go to UniProtKB:  P76116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76116
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.17α = 90
b = 139.31β = 90
c = 173.69γ = 90
Software Package:
Software NamePurpose
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Database references