6Q0C

MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with undamaged dG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY.

Russelburg, L.P.O'Shea Murray, V.L.Demir, M.Knutsen, K.R.Sehgal, S.L.Cao, S.David, S.S.Horvath, M.P.

(2020) ACS Chem Biol 15: 93-102

  • DOI: https://doi.org/10.1021/acschembio.9b00639
  • Primary Citation of Related Structures:  
    6Q0C, 6U7T

  • PubMed Abstract: 

    The adenine glycosylase MutY selectively initiates repair of OG:A lesions and, by comparison, avoids G:A mispairs. The ability to distinguish these closely related substrates relies on the C-terminal domain of MutY, which structurally resembles MutT. To understand the mechanism for substrate specificity, we crystallized MutY in complex with DNA containing G across from the high-affinity azaribose transition state analogue. Our structure shows that G is accommodated by the OG site and highlights the role of a serine residue in OG versus G discrimination. The functional significance of Ser308 and its neighboring residues was evaluated by mutational analysis, revealing the critical importance of a β loop in the C-terminal domain for mutation suppression in cells, and biochemical performance in vitro . This loop comprising residues Phe307, Ser308, and His309 ( Geobacillus stearothermophilus sequence positions) is conserved in MutY but absent in MutT and other DNA repair enzymes and may therefore serve as a MutY-specific target exploitable by chemical biological probes.


  • Organizational Affiliation

    School of Biological Sciences , University of Utah , 257 South 1400 East , Salt Lake City , Utah 84112 , United States.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A/G-specific adenine glycosylase366Geobacillus stearothermophilusMutation(s): 0 
Gene Names: MutY
EC: 3.2.2.31
UniProt
Find proteins for P83847 (Geobacillus stearothermophilus)
Explore P83847 
Go to UniProtKB:  P83847
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83847
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3')11synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')11synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.86α = 90
b = 86.14β = 90
c = 141.17γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1608934
National Science Foundation (NSF, United States)United States1610721

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Derived calculations
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Database references
  • Version 1.4: 2020-01-29
    Changes: Database references
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description