PDBsum entry 4nci

DNA binding protein

PDB id: 4nci

Contents

Protein chain

311 a.a.

Waters ×172

PDB id:

4nci

Name:

DNA binding protein

Title:

Crystal structure of pyrococcus furiosis rad50 r805e mutation

Structure:

DNA double-strand break repair rad50 atpase. Chain: a. Fragment: unp residues 1-177 and 726-882. Engineered: yes. Mutation: yes

Source:

Pyrococcus furiosus. Organism_taxid: 186497. Strain: atcc 43587 / dsm 3638 / jcm 8422 / vc1. Gene: pf1167, rad50. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.30Å R-factor: 0.204 R-free: 0.258

Authors:

S.Classen,G.J.Williams,A.S.Arvai,R.S.Williams

Key ref:

R.A.Deshpande et al. (2014). ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. Embo J, 33, 482-500. PubMed id: 24493214 DOI: 10.1002/embj.201386100

Date:

24-Oct-13 Release date: 05-Mar-14

Protein chain

P58301  (RAD50_PYRFU) -  DNA double-strand break repair Rad50 ATPase from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 882 a.a.

Struc: 311 a.a.*

* PDB and UniProt seqs differ at 123 residue positions (black crosses)

DOI no: 10.1002/embj.201386100

Embo J 33:482-500 (2014)

PubMed id: 24493214

ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.

R.A.Deshpande, G.J.Williams, O.Limbo, R.S.Williams, J.Kuhnlein, J.H.Lee, S.Classen, G.Guenther, P.Russell, J.A.Tainer, T.T.Paull.

ABSTRACT

The Mre11-Rad50 complex is highly conserved, yet the mechanisms by which Rad50 ATP-driven states regulate the sensing, processing and signaling of DNA double-strand breaks are largely unknown. Here we design structure-based mutations in Pyrococcus furiosus Rad50 to alter protein core plasticity and residues undergoing ATP-driven movements within the catalytic domains. With this strategy we identify Rad50 separation-of-function mutants that either promote or destabilize the ATP-bound state. Crystal structures, X-ray scattering, biochemical assays, and functional analyses of mutant PfRad50 complexes show that the ATP-induced 'closed' conformation promotes DNA end binding and end tethering, while hydrolysis-induced opening is essential for DNA resection. Reducing the stability of the ATP-bound state impairs DNA repair and Tel1 (ATM) checkpoint signaling in Schizosaccharomyces pombe, double-strand break resection in Saccharomyces cerevisiae, and ATM activation by human Mre11-Rad50-Nbs1 in vitro, supporting the generality of the P. furiosus Rad50 structure-based mutational analyses. These collective results suggest that ATP-dependent Rad50 conformations switch the Mre11-Rad50 complex between DNA tethering, ATM signaling, and 5' strand resection, revealing molecular mechanisms regulating responses to DNA double-strand breaks.