Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.67 kDa 
• Atom Count: 2443 
• Modelled Residue Count: 273 
• Deposited Residue Count: 273 
• Unique protein chains: 1

4MB7

Crystal Structure of a viral DNA glycosylase

• PDB DOI: 10.2210/pdb4MB7/pdb

• Classification: HYDROLASE
• Organism(s): Acanthamoeba polyphaga mimivirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-19 Released: 2013-10-30 
• Deposition Author(s): Prakash, A., Eckenroth, B.E., Doublie, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.225 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 

Literature

Structural investigation of a viral ortholog of human NEIL2/3 DNA glycosylases.

Prakash, A., Eckenroth, B.E., Averill, A.M., Imamura, K., Wallace, S.S., Doublie, S.

(2013) DNA Repair (Amst) 12: 1062-1071

• PubMed: 24120312 
• DOI: 10.1016/j.dnarep.2013.09.004
• Primary Citation of Related Structures:  
  4MB7


• PubMed Abstract: 
  

Assault to DNA that leads to oxidative base damage is repaired by the base excision repair (BER) pathway with specialized enzymes called DNA glycosylases catalyzing the first step of this pathway. These glycosylases can be categorized into two families: the HhH superfamily, which includes endonuclease III (or Nth), and the Fpg/Nei family, which comprises formamidopyrimidine DNA glycosylase (or Fpg) and endonuclease VIII (or Nei). In humans there are three Nei-like (NEIL) glycosylases: NEIL1, 2, and 3. Here we present the first crystal structure of a viral ortholog of the human NEIL2/NEIL3 proteins, Mimivirus Nei2 (MvNei2), determined at 2.04Å resolution. The C-terminal region of the MvNei2 enzyme comprises two conserved DNA binding motifs: the helix-two-turns-helix (H2TH) motif and a C-H-C-C type zinc-finger similar to that of human NEIL2. The N-terminal region of MvNei2 is most closely related to NEIL3. Like NEIL3, MvNei2 bears a valine at position 2 instead of the usual proline and it lacks two of the three conserved void-filling residues present in other members of the Fpg/Nei family. Mutational analysis of the only conserved void-filling residue methionine 72 to alanine yields an MvNei2 variant with impaired glycosylase activity. Mutation of the adjacent His73 causes the enzyme to be more productive thereby suggesting a plausible role for this residue in the DNA lesion search process.

---

Organizational Affiliation: 

Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease 8-like L720	A	273	Acanthamoeba polyphaga mimivirus	Mutation(s): 0  Gene Names: Endonuclease VIII (nei) 2, MIMI_L720 EC: 4.2.99.18 (PDB Primary Data), 3.2.2.23 (PDB Primary Data)
UniProt
Find proteins for Q5UNW7 (Acanthamoeba polyphaga mimivirus) Explore Q5UNW7  Go to UniProtKB:  Q5UNW7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.225 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.67	α = 90
b = 121.67	β = 90
c = 164.18	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
SOLVE	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-19 
• Released Date: 2013-10-30 
Deposition Author(s): Prakash, A., Eckenroth, B.E., Doublie, S.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references