7AYY | pdb_00007ayy

Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785

PDB DOI: https://doi.org/10.2210/pdb7AYY/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-13 Released: 2022-06-01
Deposition Author(s): Masuyer, G., Davies, J.R., Stenmark, P.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.250 (Depositor), 0.228 (DCC)
R-Value Work:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 35737787 Search on PubMed
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.

Instituto de Investigaciones Biomédicas Alberto Sols (CSIC/UAM), 28029 Madrid, Spain.

Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049 Madrid, Spain.

Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath BA2 7AY, UK.

Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.

Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway.

Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7465 Trondheim, Norway.

Experimental Therapies and Novel Biomarkers in Cancer, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.

Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

Department of Environment and New Resources, SINTEF Ocean, N-7496 Trondheim, Norway.

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Department of Biomolecular Chemistry, 07745 Jena, Germany.

Department of Experimental Medical Science, Lund University, Lund, Sweden.

Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.

Institute of Organic and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany.

Chemical Processes and Pharmaceutical Development, Unit Process Chemistry I, Research Institutes of Sweden - RISE, 151 36 Södertälje, Sweden.

Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden.

Familial Cancer Clinical Unit, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.

Institute of Microbiology, Friedrich-Schiller-University Jena, 07743 Jena, Germany.

Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain.

Institute of Biochemistry II and Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, 60590 Frankfurt, Germany.

Macromolecule Content

Total Structure Weight: 191.72 kDa
Atom Count: 13,010
Modeled Residue Count: 1,529
Deposited Residue Count: 1,685
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE]	337	Homo sapiens	Mutation(s): 0 Gene Names: OGG1, MMH, MUTM, OGH1 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O15527 (Homo sapiens) Explore O15527 Go to UniProtKB: O15527
PHAROS: O15527 GTEx: ENSG00000114026
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15527
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SEQ (Subject of Investigation/LOI) Query on SEQ Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain H [auth BBB] SDF format, chain J [auth CCC] SDF format, chain K [auth DDD] SDF format, chain M [auth EEE] MOL2 format, chain F [auth AAA] MOL2 format, chain H [auth BBB] MOL2 format, chain J [auth CCC] MOL2 format, chain K [auth DDD] MOL2 format, chain M [auth EEE] mmCIF format, chain F [auth AAA] mmCIF format, chain H [auth BBB] mmCIF format, chain J [auth CCC] mmCIF format, chain K [auth DDD] mmCIF format, chain M [auth EEE]	F [auth AAA], H [auth BBB], J [auth CCC], K [auth DDD], M [auth EEE]	~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine C₁₇ H₂₁ N₃ ZQMGQZOHIDOPCQ-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain H [auth BBB] Focus chain J [auth CCC] Focus chain K [auth DDD] Focus chain M [auth EEE] Interactions & Density Focus chain F [auth AAA] Focus chain H [auth BBB] Focus chain J [auth CCC] Focus chain K [auth DDD] Focus chain M [auth EEE]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain I [auth BBB] SDF format, chain N [auth EEE] MOL2 format, chain G [auth AAA] MOL2 format, chain I [auth BBB] MOL2 format, chain N [auth EEE] mmCIF format, chain G [auth AAA] mmCIF format, chain I [auth BBB] mmCIF format, chain N [auth EEE]	G [auth AAA], I [auth BBB], N [auth EEE]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain I [auth BBB] Focus chain N [auth EEE] Interactions & Density Focus chain G [auth AAA] Focus chain I [auth BBB] Focus chain N [auth EEE]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth DDD] SDF format, chain O [auth EEE] MOL2 format, chain L [auth DDD] MOL2 format, chain O [auth EEE] mmCIF format, chain L [auth DDD] mmCIF format, chain O [auth EEE]	L [auth DDD], O [auth EEE]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth DDD] Focus chain O [auth EEE] Interactions & Density Focus chain L [auth DDD] Focus chain O [auth EEE]