2BGW

XPF from Aeropyrum pernix, complex with DNA

Summary for 2BGW

• Entry DOI: 10.2210/pdb2bgw/pdb
• Descriptor: XPF ENDONUCLEASE, 5'-D(*GP*AP*TP*CP*AP*CP*AP*GP*AP*TP *GP*CP*TP*GP*A)-3', 5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP *TP*GP*AP*TP*C)-3', ... (6 entities in total)
• Functional Keywords: hydrolase, structure specific endonuclease, nucleotide excision repair
• Biological source: Aeropyrum pernix; More
• Total number of polymer chains: 4
• Total formula weight: 59792.55

Authors

Newman, M.,Murray-Rust, J.,Lally, J.,Rudolf, J.,Fadden, A.,Knowles, P.P.,White, M.F.,McDonald, N.Q. (deposition date: 2005-01-06, release date: 2005-02-23, Last modification date: 2023-12-13)

Primary citation

Newman, M.,Murray-Rust, J.,Lally, J.,Rudolf, J.,Fadden, A.,Knowles, P.P.,White, M.F.,McDonald, N.Q.
Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.
EMBO J., 24:895-905, 2005

PubMed Abstract: The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an archaeal XPF homodimer alone and bound to dsDNA. Superposition of these structures reveals a large domain movement upon binding DNA, indicating how the (HhH)(2) domain and the nuclease domain are coupled to allow the recognition of double-stranded/single-stranded DNA junctions. We identify two nonequivalent DNA-binding sites and propose a model in which XPF distorts the 3' flap substrate in order to engage both binding sites and promote strand cleavage. The model rationalises published biochemical data and implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes.

PubMed: 15719018
DOI: 10.1038/sj.emboj.7600581

Experimental method

X-RAY DIFFRACTION (2.8 Å)