4MB7

Crystal Structure of a viral DNA glycosylase

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 

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This is version 1.1 of the entry. See complete history. 


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

  • 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) ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease 8-like L720A273Acanthamoeba polyphaga mimivirusMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
 C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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 = 121.67α = 90
b = 121.67β = 90
c = 164.18γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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