5DPK

MutY adenine glycosylase bound to a transition state analog (1N) paired with d(8-oxoG) in duplexed DNA to 2.2 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.

Woods, R.D.O'Shea, V.L.Chu, A.Cao, S.Richards, J.L.Horvath, M.P.David, S.S.

(2016) Nucleic Acids Res. 44: 801-810

  • DOI: 10.1093/nar/gkv1469

  • PubMed Abstract: 
  • MutY adenine glycosylases prevent DNA mutations by excising adenine from promutagenic 8-oxo-7,8-dihydroguanine (OG):A mismatches. Here, we describe structural features of the MutY active site bound to an azaribose transition state analog which indica ...

    MutY adenine glycosylases prevent DNA mutations by excising adenine from promutagenic 8-oxo-7,8-dihydroguanine (OG):A mismatches. Here, we describe structural features of the MutY active site bound to an azaribose transition state analog which indicate a catalytic role for Tyr126 and approach of the water nucleophile on the same side as the departing adenine base. The idea that Tyr126 participates in catalysis, recently predicted by modeling calculations, is strongly supported by mutagenesis and by seeing close contact between the hydroxyl group of this residue and the azaribose moiety of the transition state analog. NMR analysis of MutY methanolysis products corroborates a mechanism for adenine removal with retention of stereochemistry. Based on these results, we propose a revised mechanism for MutY that involves two nucleophilic displacement steps akin to the mechanisms accepted for 'retaining' O-glycosidases. This new-for-MutY yet familiar mechanism may also be operative in related base excision repair glycosylases and provides a critical framework for analysis of human MutY (MUTYH) variants associated with inherited colorectal cancer.


    Organizational Affiliation

    Department of Chemistry, University of California, Davis, CA 95616, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A/G-specific adenine glycosylase
A
366Geobacillus stearothermophilusGene Names: mutY
EC: 3.2.2.-
Find proteins for P83847 (Geobacillus stearothermophilus)
Go to UniProtKB:  P83847
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')B11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')C11synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
B
DNA LINKINGC10 H14 N5 O8 PDG
NR1
Query on NR1
C
DNA linkingC5 H13 N O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.850α = 90.00
b = 86.620β = 90.00
c = 140.770γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA067985

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references
  • Version 1.2: 2015-12-30
    Type: Database references
  • Version 1.3: 2016-02-10
    Type: Database references
  • Version 1.4: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations