9BS2 | pdb_00009bs2

Glycosylase MutY variant R149Q in complex with DNA containing d(8-oxo-G) paired with a product analog (THF) to 1.51 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair.

Trasvina-Arenas, C.H.Dissanayake, U.C.Tamayo, N.Hashemian, M.Lin, W.J.Demir, M.Hoyos-Gonzalez, N.Fisher, A.J.Cisneros, G.A.Horvath, M.P.David, S.S.

(2025) Nat Commun 16: 3596-3596

  • DOI: https://doi.org/10.1038/s41467-025-58361-w
  • Primary Citation of Related Structures:  
    8FAY, 9BS2

  • PubMed Abstract: 

    MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor reveals that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal cluster and bound substrate DNA tightly, but were completely inactive. We determine the crystal structure of human MUTYH bound to a transition state mimic and this shows that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, support a model in which the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site of MUTYH regulate its DNA repair function.


  • Organizational Affiliation
    • Department of Chemistry, University of California, Davis, CA, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenine DNA glycosylase369Geobacillus stearothermophilusMutation(s): 1 
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
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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(*TP*GP*TP*CP*CP*AP*(3DR)P*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: 1.51 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.5α = 90
b = 86β = 90
c = 140.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2204228
National Science Foundation (NSF, United States)United States2204229
National Science Foundation (NSF, United States)United States1905249
National Science Foundation (NSF, United States)United States1905304

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references