9BPA

Human DNA polymerase theta helicase domain in complex with inhibitor AB25583, tetramer form

Summary for 9BPA

• Entry DOI: 10.2210/pdb9bpa/pdb
• EMDB information: 44766
• Descriptor: DNA polymerase theta, (4P)-N-{5-[(4-chlorophenyl)methoxy]-1,3,4-thiadiazol-2-yl}-4-(2-methoxyphenyl)pyridine-3-carboxamide (2 entities in total)
• Functional Keywords: dna repair, helicase, atpase, transferase-inhibitor complex, transferase/inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 4
• Total formula weight: 401021.81

Authors

Ito, F.,Li, Z.,Chen, X.S. (deposition date: 2024-05-07, release date: 2024-08-28)

Primary citation

Ito, F.,Li, Z.,Minakhin, L.,Chandramouly, G.,Tyagi, M.,Betsch, R.,Krais, J.J.,Taberi, B.,Vekariya, U.,Calbert, M.,Skorski, T.,Johnson, N.,Chen, X.S.,Pomerantz, R.T.
Structural basis for a Pol theta helicase small-molecule inhibitor revealed by cryo-EM.
Nat Commun, 15:7003-7003, 2024

PubMed Abstract: DNA polymerase theta (Polθ) is a DNA helicase-polymerase protein that facilitates DNA repair and is synthetic lethal with homology-directed repair (HDR) factors. Thus, Polθ is a promising precision oncology drug-target in HDR-deficient cancers. Here, we characterize the binding and mechanism of action of a Polθ helicase (Polθ-hel) small-molecule inhibitor (AB25583) using cryo-EM. AB25583 exhibits 6 nM IC against Polθ-hel, selectively kills BRCA1/2-deficient cells, and acts synergistically with olaparib in cancer cells harboring pathogenic BRCA1/2 mutations. Cryo-EM uncovers predominantly dimeric Polθ-hel:AB25583 complex structures at 3.0-3.2 Å. The structures reveal a binding-pocket deep inside the helicase central-channel, which underscores the high specificity and potency of AB25583. The cryo-EM structures in conjunction with biochemical data indicate that AB25583 inhibits the ATPase activity of Polθ-hel helicase via an allosteric mechanism. These detailed structural data and insights about AB25583 inhibition pave the way for accelerating drug development targeting Polθ-hel in HDR-deficient cancers.

PubMed: 39143110
DOI: 10.1038/s41467-024-51351-4

Experimental method

ELECTRON MICROSCOPY (3.21 Å)