5ITQ

Crystal Structure of Human NEIL1, Free Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

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 U S A 113: 7792-7797

  • DOI: 10.1073/pnas.1604591113
  • Primary Citation of Related Structures:  
    5ITY, 5ITX, 5ITQ, 5ITR, 5ITU, 5ITT

  • 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 present crystal structures of human NEIL1 bound to a range of duplex DNA ...

    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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease 8-like 1A290Homo sapiensMutation(s): 2 
Gene Names: NEIL1
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FI4 (Homo sapiens)
Explore Q96FI4 
Go to UniProtKB:  Q96FI4
PHAROS:  Q96FI4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.454α = 90
b = 132.454β = 90
c = 50.791γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Foundation of ChinaChina2014CB964900
National Natural Science Foundation of ChinaChina31270838
National Natural Science Foundation of China21522201

Revision History  (Full details and data files)

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