5ITR

Crystal Structure of Human NEIL1(P2G) bound to duplex DNA containing THF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair

Zhu, C.Lu, L.Zhang, J.Yue, Z.Song, J.Zong, S.Liu, M.Stovicek, O.Gao, Y.Q.Yi, C.

(2016) Proc.Natl.Acad.Sci.USA 113: 7792-7797

  • DOI: 10.1073/pnas.1604591113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome against oxidized DNA bases. As the first enzymes in the base-excision repair pathway, glycosylases must recognize the cognate substrates and catalyze their excision. Here we ...

    NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome against oxidized DNA bases. As the first enzymes in the base-excision repair pathway, glycosylases must recognize the cognate substrates and catalyze their excision. Here we present crystal structures of human NEIL1 bound to a range of duplex DNA. Together with computational and biochemical analyses, our results suggest that NEIL1 promotes tautomerization of thymine glycol (Tg)-a preferred substrate-for optimal binding in its active site. Moreover, this tautomerization event also facilitates NEIL1-catalyzed Tg excision. To our knowledge, the present example represents the first documented case of enzyme-promoted tautomerization for efficient substrate recognition and catalysis in an enzyme-catalyzed reaction.


    Organizational Affiliation

    Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China;,University of Chicago, Chicago, IL 60637;,Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China; gaoyq@pku.edu.cn chengqi.yi@pku.edu.cn.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China gaoyq@pku.edu.cn chengqi.yi@pku.edu.cn.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China;,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endonuclease 8-like 1
A, B, C
400Homo sapiensMutation(s): 1 
Gene Names: NEIL1
EC: 3.2.2.-, 4.2.99.18
Find proteins for Q96FI4 (Homo sapiens)
Go to Gene View: NEIL1
Go to UniProtKB:  Q96FI4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (26-MER)D,E26unidentified
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (26-MER)F26unidentified
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.306α = 90.00
b = 109.036β = 90.00
c = 169.837γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references