8GD7 | pdb_00008gd7

Loop Deleted DNA Polymerase Theta Polymerase Domain in Complex with Double Strand DNA Overhang and Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8GD7/pdb
• NAKB: 8GD7

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-03 Released: 2024-06-19 
• Deposition Author(s): Fried, W.A., Chen, X.S., Li, S.X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 
  0.244 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Discovery of a small-molecule inhibitor that traps Pol theta on DNA and synergizes with PARP inhibitors.

Fried, W., Tyagi, M., Minakhin, L., Chandramouly, G., Tredinnick, T., Ramanjulu, M., Auerbacher, W., Calbert, M., Rusanov, T., Hoang, T., Borisonnik, N., Betsch, R., Krais, J.J., Wang, Y., Vekariya, U.M., Gordon, J., Morton, G., Kent, T., Skorski, T., Johnson, N., Childers, W., Chen, X.S., Pomerantz, R.T.

(2024) Nat Commun 15: 2862-2862

• PubMed: 38580648 
• DOI: https://doi.org/10.1038/s41467-024-46593-1
• Primary Citation Related Structures: 
  8GD7


• PubMed Abstract: 
  

  The DNA damage response (DDR) protein DNA Polymerase θ (Polθ) is synthetic lethal with homologous recombination (HR) factors and is therefore a promising drug target in BRCA1/2 mutant cancers. We discover an allosteric Polθ inhibitor (Polθi) class with 4-6 nM IC ₅₀ that selectively kills HR-deficient cells and acts synergistically with PARP inhibitors (PARPi) in multiple genetic backgrounds. X-ray crystallography and biochemistry reveal that Polθi selectively inhibits Polθ polymerase (Polθ-pol) in the closed conformation on B-form DNA/DNA via an induced fit mechanism. In contrast, Polθi fails to inhibit Polθ-pol catalytic activity on A-form DNA/RNA in which the enzyme binds in the open configuration. Remarkably, Polθi binding to the Polθ-pol:DNA/DNA closed complex traps the polymerase on DNA for more than forty minutes which elucidates the inhibitory mechanism of action. These data reveal a unique small-molecule DNA polymerase:DNA trapping mechanism that induces synthetic lethality in HR-deficient cells and potentiates the activity of PARPi.

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Organizational Affiliation: 
• Molecular and Computational Biology, Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA.
Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA.
Fels Cancer Institute for Personalized Medicine, Philadelphia, PA, USA.
Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
Janssen Biotech, Malvern, PA, 19355, USA.
Polysciences, Inc., Huntingdon Valley, PA, USA.
Nuclear Dynamics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
Department of Cancer and Cellular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, USA.
Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA. [e-mail].
Recombination Therapeutics, Pennsylvania Biotechnology Center, Doylestown, PA, 18902, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.22 kDa 
• Atom Count: 5,514 
• Modeled Residue Count: 654 
• Deposited Residue Count: 690 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase theta	A	652	Homo sapiens	Mutation(s): 0  Gene Names: POLQ EC: 2.7.7.7 (PDB Primary Data), 3.6.4.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75417 (Homo sapiens) Explore O75417  Go to UniProtKB:  O75417
PHAROS:  O75417 GTEx:  ENSG00000051341

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA Template	B [auth E]	24	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA Primer	C [auth F]	14	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DG3	E [auth A]	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O12 P3 HDRRAMINWIWTNU-NTSWFWBYSA-N
Z5X (Subject of Investigation/LOI)	F [auth A]	2-(3-methyl-2-oxoimidazolidin-1-yl)-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)methylcarbamate C20 H16 F7 N3 O3 OMLNQKKHSWHSNR-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free:  0.244 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.433	α = 90
b = 171.433	β = 90
c = 63.167	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Coot	model building
HKL-2000	data scaling
HKL-2000	data reduction
JBluIce-EPICS	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Fried, W.A., Chen, X.S., Li, S.X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM130889

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release