4O4K | pdb_00004o4k

DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities

• PDB DOI: https://doi.org/10.2210/pdb4O4K/pdb

• Classification: DNA BINDING PROTEIN/inhibitor
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-18 Released: 2014-01-08 
• Deposition Author(s): Shibata, A., Moiani, D., Arvai, A.S., Perry, J., Harding, S.M., Genois, M., Maity, R., Rossum-Fikkert, S., Kertokalio, A., Romoli, F., Ismail, A., Ismalaj, E., Petricci, E., Neale, M.J., Bristow, R.G., Masson, J., Wyman, C., Jeggo, P.A., Tainer, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities.

Shibata, A., Moiani, D., Arvai, A.S., Perry, J., Harding, S.M., Genois, M.M., Maity, R., van Rossum-Fikkert, S., Kertokalio, A., Romoli, F., Ismail, A., Ismalaj, E., Petricci, E., Neale, M.J., Bristow, R.G., Masson, J.Y., Wyman, C., Jeggo, P.A., Tainer, J.A.

(2014) Mol Cell 53: 7-18

• PubMed: 24316220 
• DOI: https://doi.org/10.1016/j.molcel.2013.11.003
• Primary Citation Related Structures: 
  4NZV, 4O24, 4O43, 4O4K, 4O5G


• PubMed Abstract: 
  

  MRE11 within the MRE11-RAD50-NBS1 (MRN) complex acts in DNA double-strand break repair (DSBR), detection, and signaling; yet, how its endo- and exonuclease activities regulate DSBR by nonhomologous end-joining (NHEJ) versus homologous recombination (HR) remains enigmatic. Here, we employed structure-based design with a focused chemical library to discover specific MRE11 endo- or exonuclease inhibitors. With these inhibitors, we examined repair pathway choice at DSBs generated in G2 following radiation exposure. While nuclease inhibition impairs radiation-induced replication protein A (RPA) chromatin binding, suggesting diminished resection, the inhibitors surprisingly direct different repair outcomes. Endonuclease inhibition promotes NHEJ in lieu of HR, while exonuclease inhibition confers a repair defect. Collectively, the results describe nuclease-specific MRE11 inhibitors, define distinct nuclease roles in DSB repair, and support a mechanism whereby MRE11 endonuclease initiates resection, thereby licensing HR followed by MRE11 exonuclease and EXO1/BLM bidirectional resection toward and away from the DNA end, which commits to HR.

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Organizational Affiliation: 
• Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK; Advanced Scientific Research Leaders Development Unit, Gunma University, Maebashi, Gunma 371-8511, Japan.
Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; The School of Biotechnology, Amrita University, Kollam, Kerala 690525, India.
Departments of Radiation Oncology and Medical Biophysics, University of Toronto, ON M5G 2M9, Canada.
Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, 9 McMahon, QC G1R 2J6, Canada.
Department of Radiation Oncology, Department of Genetics, Erasmus University Medical Center, P.O. Box 2040, Rotterdam 3000 CA, the Netherlands.
Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy.
Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.
Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK. Electronic address: [e-mail].
Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.81 kDa 
• Atom Count: 5,318 
• Modeled Residue Count: 652 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exonuclease, putative	A, B	336	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_1635 EC: 3.1
UniProt
Find proteins for Q9X1X0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1X0  Go to UniProtKB:  Q9X1X0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PK	E [auth A], H [auth B]	(5~{E})-2-azanylidene-5-[(4-hydroxyphenyl)methylidene]-1,3-thiazolidin-4-one C10 H8 N2 O2 S YBHQCJILTOVLHD-VMPITWQZSA-N
MN	C [auth A], D [auth A], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.769	α = 90
b = 113.154	β = 101.47
c = 80.891	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-08 
Deposition Author(s): Shibata, A., Moiani, D., Arvai, A.S., Perry, J., Harding, S.M., Genois, M., Maity, R., Rossum-Fikkert, S., Kertokalio, A., Romoli, F., Ismail, A., Ismalaj, E., Petricci, E., Neale, M.J., Bristow, R.G., Masson, J., Wyman, C., Jeggo, P.A., Tainer, J.A.

Revision History  

• Version 1.0: 2014-01-08
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 2.0: 2020-02-19
  Changes: Advisory, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description