4B21

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2.

Dalhus, B.Nilsen, L.Korvald, H.Huffman, J.Forstrom, R.J.Mcmurray, C.T.Alseth, I.Tainer, J.A.Bjoras, M.

(2013) Structure 21: 154

  • DOI: 10.1016/j.str.2012.11.004
  • Primary Citation of Related Structures:  4B22, 4B23, 4B24

  • PubMed Abstract: 
  • Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which fu ...

    Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which further pass on nicked DNA to downstream DNA polymerases and ligases. The coordinated handover of cytotoxic intermediates between different BER enzymes is most likely facilitated by the DNA conformation. Here, we present the atomic structure of Schizosaccharomyces pombe Mag2 in complex with DNA to reveal an unexpected structural basis for nonenzymatic AP site recognition with an unflipped AP site. Two surface-exposed loops intercalate and widen the DNA minor groove to generate a DNA conformation previously only found in the mismatch repair MutS-DNA complex. Consequently, the molecular role of Mag2 appears to be AP site recognition and protection, while possibly facilitating damage signaling by structurally sculpting the DNA substrate.


    Organizational Affiliation

    Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2
A
232Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: mag2
EC: 3.2.2.21
Find proteins for O94468 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94468
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3'X11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'Y10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, Y
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
X
DNA LINKINGC5 H11 O6 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.207 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 68.926α = 90.00
b = 84.746β = 90.00
c = 126.713γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references