5ITX

Crystal Structure of Human NEIL1(P2G R242K) bound to duplex DNA containing Thymine Glycol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1073/pnas.1604591113
  • Primary Citation of Related Structures:  
    5ITQ, 5ITR, 5ITT, 5ITU, 5ITX, 5ITY

  • 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. 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endonuclease 8-like 1A,
C [auth B]
390Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000140398 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96FI4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Endonuclease 8-like 1400Homo 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
GTEx:  ENSG00000140398 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96FI4
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (26-MER)B [auth D],
D [auth C],
F
26unidentified
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.991α = 90
b = 109.378β = 90
c = 170.968γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description