5ITY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 

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

    State Key Laboratory of Protein and Plant Gene Research, School of 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): 2 
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,E,F26unidentified
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CTG
Query on CTG
D, E, F
DNA LINKINGC10 H17 N2 O10 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.624α = 90.00
b = 108.706β = 90.00
c = 169.972γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PHASERphasing
HKL-2000data 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