Structure of mammalian NEIL2 from Monodelphis domestica

Experimental Data Snapshot

  • Resolution: 2.54 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

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This is version 1.2 of the entry. See complete history


Unique Structural Features of Mammalian NEIL2 DNA Glycosylase Prime Its Activity for Diverse DNA Substrates and Environments.

Eckenroth, B.E.Cao, V.B.Averill, A.M.Dragon, J.A.Doublie, S.

(2021) Structure 29: 29-42.e4

  • DOI: https://doi.org/10.1016/j.str.2020.08.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Oxidative damage on DNA arising from both endogenous and exogenous sources can result in base modifications that promote errors in replication as well as generating sites of base loss (abasic sites) that present unique challenges to maintaining genomic integrity. These lesions are excised by DNA glycosylases in the first step of the base excision repair pathway. Here we present the first crystal structure of a NEIL2 glycosylase, an enzyme active on cytosine oxidation products and abasic sites. The structure reveals an unusual "open" conformation not seen in NEIL1 or NEIL3 orthologs. NEIL2 is predicted to adopt a "closed" conformation when bound to its substrate. Combined crystallographic and solution-scattering studies show the enzyme to be conformationally dynamic in a manner distinct among the NEIL glycosylases and provide insight into the unique substrate preference of this enzyme. In addition, we characterized three cancer variants of human NEIL2, namely S140N, G230W, and G303R.

  • Organizational Affiliation

    Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA. Electronic address: beckenro@uvm.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nei like DNA glycosylase 2
A, B
344Monodelphis domesticaMutation(s): 0 
Gene Names: NEIL2
Find proteins for F7AMK3 (Monodelphis domestica)
Explore F7AMK3 
Go to UniProtKB:  F7AMK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7AMK3
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.54 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: P 32
  • Diffraction Data: https://doi.org/10.18430/m36vji
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.887α = 90
b = 67.887β = 90
c = 149.13γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA098993
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA233185

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references