4B5F

Substrate bound Neisseria AP endonuclease in absence of metal ions (crystal form 1)

Summary for 4B5F

• Entry DOI: 10.2210/pdb4b5f/pdb
• Related: 4B5G 4B5H 4B5I 4B5J 4B5M
• Descriptor: PUTATIVE EXODEOXYRIBONUCLEASE, 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3', 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*CP)-3', ... (4 entities in total)
• Functional Keywords: hydrolase-dna complex, hydrolase/dna
• Biological source: NEISSERIA MENINGITIDIS; More
• Total number of polymer chains: 3
• Total formula weight: 36298.90

Authors

Lu, D.,Silhan, J.,MacDonald, J.T.,Carpenter, E.P.,Jensen, K.,Tang, C.M.,Baldwin, G.S.,Freemont, P.S. (deposition date: 2012-08-03, release date: 2012-10-17, Last modification date: 2024-05-08)

Primary citation

Lu, D.,Silhan, J.,MacDonald, J.T.,Carpenter, E.P.,Jensen, K.,Tang, C.M.,Baldwin, G.S.,Freemont, P.S.
Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Proc. Natl. Acad. Sci. U.S.A., 109:16852-16857, 2012

PubMed Abstract: Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures.

PubMed: 23035246
DOI: 10.1073/pnas.1206563109

Experimental method

X-RAY DIFFRACTION (2.005 Å)