6VJI | pdb_00006vji

Structure of mammalian NEIL2 from Monodelphis domestica

• PDB DOI: https://doi.org/10.2210/pdb6VJI/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Monodelphis domestica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-16 Released: 2020-08-12 
• Deposition Author(s): Eckenroth, B.E., Doublie, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.275 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Literature

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

• PubMed: 32846144 
• DOI: https://doi.org/10.1016/j.str.2020.08.001
• Primary Citation Related Structures: 
  6VJI


• 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.

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Organizational Affiliation: 
• Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA. Electronic address: [e-mail].
Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA.
Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79 kDa 
• Atom Count: 3,815 
• Modeled Residue Count: 508 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nei like DNA glycosylase 2	A, B	344	Monodelphis domestica	Mutation(s): 0  Gene Names: NEIL2 EC: 4.2.99.18
UniProt
Find proteins for F7AMK3 (Monodelphis domestica) Explore F7AMK3  Go to UniProtKB:  F7AMK3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.275 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36vji

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.887	α = 90
b = 67.887	β = 90
c = 149.13	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHARP	phasing
SOLOMON	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Eckenroth, B.E., Doublie, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA098993
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA233185

Revision History  

• 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
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Refinement description, Structure summary