3S6I

Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.

Adhikary, S.Eichman, B.F.

(2011) Embo Rep. 12: 1286-1292

  • DOI: 10.1038/embor.2011.189

  • PubMed Abstract: 
  • DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed ...

    DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N(6)-ethenoadenine (ɛA) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their ɛA activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.


    Organizational Affiliation

    Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Box 351634 Station B, 5270A MRBIII, Nashville, Tennessee 37235, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-3-methyladenine glycosylase 1
A, D
228Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: mag1
EC: 3.2.2.21
Find proteins for Q92383 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q92383
Entity ID: 2
MoleculeChainsLengthOrganism
(5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')B,E11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
(5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')C,F11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
B, E
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.317α = 90.00
b = 112.298β = 99.55
c = 61.113γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SHARPphasing
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release