7AZ0 | pdb_00007az0

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with TH12161


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.257 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.237 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function.

Michel, M.Benitez-Buelga, C.Calvo, P.A.Hanna, B.M.F.Mortusewicz, O.Masuyer, G.Davies, J.Wallner, O.Sanjiv, K.Albers, J.J.Castaneda-Zegarra, S.Jemth, A.S.Visnes, T.Sastre-Perona, A.Danda, A.N.Homan, E.J.Marimuthu, K.Zhenjun, Z.Chi, C.N.Sarno, A.Wiita, E.von Nicolai, C.Komor, A.J.Rajagopal, V.Muller, S.Hank, E.C.Varga, M.Scaletti, E.R.Pandey, M.Karsten, S.Haslene-Hox, H.Loevenich, S.Marttila, P.Rasti, A.Mamonov, K.Ortis, F.Schomberg, F.Loseva, O.Stewart, J.D'Arcy-Evans, N.Koolmeister, T.Henriksson, M.Michel, D.de Ory, A.Acero, L.Calvete, O.Scobie, M.Hertweck, C.Vilotijevic, I.Kalderen, C.Osorio, A.Perona, R.Stolz, A.Stenmark, P.Berglund, U.W.de Vega, M.Helleday, T.

(2022) Science 376: 1471-1476

  • DOI: https://doi.org/10.1126/science.abf8980
  • Primary Citation Related Structures: 
    7AYY, 7AYZ, 7AZ0

  • PubMed Abstract: 

    Oxidative DNA damage is recognized by 8-oxoguanine (8-oxoG) DNA glycosylase 1 (OGG1), which excises 8-oxoG, leaving a substrate for apurinic endonuclease 1 (APE1) and initiating repair. Here, we describe a small molecule (TH10785) that interacts with the phenylalanine-319 and glycine-42 amino acids of OGG1, increases the enzyme activity 10-fold, and generates a previously undescribed β,δ-lyase enzymatic function. TH10785 controls the catalytic activity mediated by a nitrogen base within its molecular structure. In cells, TH10785 increases OGG1 recruitment to and repair of oxidative DNA damage. This alters the repair process, which no longer requires APE1 but instead is dependent on polynucleotide kinase phosphatase (PNKP1) activity. The increased repair of oxidative DNA lesions with a small molecule may have therapeutic applications in various diseases and aging.


  • Organizational Affiliation
    • Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 76 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 108.28 kDa 
  • Atom Count: 7,481 
  • Modeled Residue Count: 929 
  • Deposited Residue Count: 954 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-glycosylase/DNA lyaseA [auth AAA],
B [auth BBB],
C [auth CCC]
318Mus musculusMutation(s): 0 
Gene Names: Ogg1
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for O08760 (Mus musculus)
Explore O08760 
Go to UniProtKB:  O08760
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08760
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.257 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.237 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.086α = 90
b = 81.645β = 90
c = 169.631γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description