3A46

Crystal structure of MvNei1/THF complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Characterization of a Viral NEIL1 Ortholog Unliganded and Bound to Abasic Site-containing DNA

Imamura, K.Wallace, S.S.Doublie, S.

(2009) J.Biol.Chem. 284: 26174-26183

  • DOI: 10.1074/jbc.M109.021907
  • Primary Citation of Related Structures:  3A42, 3A45
  • Also Cited By: 3VK7, 3VK8

  • PubMed Abstract: 
  • Endonuclease VIII (Nei) is a DNA glycosylase of the base excision repair pathway that recognizes and excises oxidized pyrimidines. We determined the crystal structures of a NEIL1 ortholog from the giant Mimivirus (MvNei1) unliganded and bound to DNA ...

    Endonuclease VIII (Nei) is a DNA glycosylase of the base excision repair pathway that recognizes and excises oxidized pyrimidines. We determined the crystal structures of a NEIL1 ortholog from the giant Mimivirus (MvNei1) unliganded and bound to DNA containing tetrahydrofuran (THF), which is the first structure of any Nei with an abasic site analog. The MvNei1 structures exhibit the same overall architecture as other enzymes of the Fpg/Nei family, which consists of two globular domains joined by a linker region. MvNei1 harbors a zincless finger, first described in human NEIL1, rather than the signature zinc finger generally found in the Fpg/Nei family. In contrast to Escherichia coli Nei, where a dramatic conformational change was observed upon binding DNA, the structure of MvNei1 bound to DNA does not reveal any substantial movement compared with the unliganded enzyme. A protein segment encompassing residues 217-245 in MvNei1 corresponds to the "missing loop" in E. coli Nei and the "alphaF-beta10 loop" in E. coli Fpg, which has been reported to be involved in lesion recognition. Interestingly, the corresponding loop in MvNei1 is ordered in both the unliganded and furan-bound structures, unlike other Fpg/Nei enzymes where the loop is generally ordered in the unliganded enzyme or in complexes with a lesion, and disordered otherwise. In the MvNei1.tetrahydrofuran complex a tyrosine located at the tip of the putative lesion recognition loop stacks against the furan ring; the tyrosine is predicted to adopt a different conformation to accommodate a modified base.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405-0068, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formamidopyrimidine-DNA glycosylase
A, B
289Acanthamoeba polyphaga mimivirusEC: 3.2.2.23, 4.2.99.18
Find proteins for Q5UQ00 (Acanthamoeba polyphaga mimivirus)
Go to UniProtKB:  Q5UQ00
Entity ID: 2
MoleculeChainsLengthOrganism
DNAC,E13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNAD,F13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
D, F
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.513α = 90.00
b = 121.462β = 95.50
c = 80.510γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance