2R9L

Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA

Summary for 2R9L

• Entry DOI: 10.2210/pdb2r9l/pdb
• Related: 2IRU 2IRX 2IRY
• Descriptor: DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3'), DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3'), DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3'), ... (7 entities in total)
• Functional Keywords: transferase, protein-dna complex, atp-binding, ligase, nucleotide-binding, transferase-dna complex, transferase/dna
• Biological source: Mycobacterium tuberculosis H37Rv; More
• Total number of polymer chains: 6
• Total formula weight: 76445.64

Authors

Brissett, N.C.,Fox, G.C.,Pitcher, R.S.,Doherty, A.J. (deposition date: 2007-09-13, release date: 2008-01-08, Last modification date: 2023-08-30)

Primary citation

Brissett, N.C.,Pitcher, R.S.,Juarez, R.,Picher, A.J.,Green, A.J.,Dafforn, T.R.,Fox, G.C.,Blanco, L.,Doherty, A.J.
Structure of a NHEJ polymerase-mediated DNA synaptic complex
Science, 318:456-459, 2007

PubMed Abstract: Nonhomologous end joining (NHEJ) is a critical DNA double-strand break (DSB) repair pathway required to maintain genome stability. Many prokaryotes possess a minimalist NHEJ apparatus required to repair DSBs during stationary phase, composed of two conserved core proteins, Ku and ligase D (LigD). The crystal structure of Mycobacterium tuberculosis polymerase domain of LigD mediating the synapsis of two noncomplementary DNA ends revealed a variety of interactions, including microhomology base pairing, mismatched and flipped-out bases, and 3' termini forming hairpin-like ends. Biochemical and biophysical studies confirmed that polymerase-induced end synapsis also occurs in solution. We propose that this DNA synaptic structure reflects an intermediate bridging stage of the NHEJ process, before end processing and ligation, with both the polymerase and the DNA sequence playing pivotal roles in determining the sequential order of synapsis and remodeling before end joining.

PubMed: 17947582
DOI: 10.1126/science.1145112

Experimental method

X-RAY DIFFRACTION (2.4 Å)