4YOQ

Crystal Structure of MutY bound to its anti-substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.

Wang, L.Lee, S.J.Verdine, G.L.

(2015) J Biol Chem 290: 17096-17105

  • DOI: https://doi.org/10.1074/jbc.M115.657866
  • Primary Citation of Related Structures:  
    4YOQ, 4YPH, 4YPR

  • PubMed Abstract: 

    The highly mutagenic A:oxoG (8-oxoguanine) base pair in DNA most frequently arises by aberrant replication of the primary oxidative lesion C:oxoG. This lesion is particularly insidious because neither of its constituent nucleobases faithfully transmit genetic information from the original C:G base pair. Repair of A:oxoG is initiated by adenine DNA glycosylase, which catalyzes hydrolytic cleavage of the aberrant A nucleobase from the DNA backbone. These enzymes, MutY in bacteria and MUTYH in humans, scrupulously avoid processing of C:oxoG because cleavage of the C residue in C:oxoG would actually promote mutagenic conversion to A:oxoG. Here we analyze the structural basis for rejection of C:oxoG by MutY, using a synthetic crystallography approach to capture the enzyme in the process of inspecting the C:oxoG anti-substrate, with which it ordinarily binds only fleetingly. We find that MutY uses two distinct strategies to avoid presentation of C to the enzyme active site. Firstly, MutY possesses an exo-site that serves as a decoy for C, and secondly, repulsive forces with a key active site residue prevent stable insertion of C into the nucleobase recognition pocket within the enzyme active site.


  • Organizational Affiliation

    From the Departments of Chemistry and Chemical Biology.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A/G-specific adenine glycosylase369Geobacillus stearothermophilusMutation(s): 2 
EC: 3.2.2
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
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')11synthetic construct
Sequence Annotations
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  • Reference Sequence

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.697α = 90
b = 84.594β = 90
c = 142.457γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-06-03
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy