3VGZ

Crystal structure of E. coli YncE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.,Sect.D 67: 1045-1053

  • DOI: 10.1107/S0907444911045033
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YncE
A, B, C, D
353Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yncE
Find proteins for P76116 (Escherichia coli (strain K12))
Go to UniProtKB:  P76116
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 119.170α = 90.00
b = 139.310β = 90.00
c = 173.690γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
CNSrefinement
BSSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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