4B5I: Product complex of Neisseria AP endonuclease in presence of metal ions

Citation:
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.
PDB ID: 4B5IDownload
MMDB ID: 104022
PDB Deposition Date: 2012/8/3
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.555  Å
Source Organism:
Neisseria meningitidis
Similar Structures:
Biological Unit for 4B5I: tetrameric; determined by author and by software (PISA)
Molecular Components in 4B5I
Label Count Molecule
Protein (1 molecule)
1
Putative Exodeoxyribonuclease
Molecule annotation
Nucleotides(3 molecules)
1
5'-d(*gp*cp*tp*ap*cp)-3'
Molecule annotation
1
5'-d(*cp*gp*ap*tp*gp*gp*gp*tp*ap*gp*cp)-3'
Molecule annotation
1
5'-d(*3drp*cp*ap*tp*cp*gp)-3'
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.