Summary
PDB 1E9N deposited: 2000-10-24 modified: 2009-02-24
Title A SECOND DIVALENT METAL ION IN THE ACTIVE SITE OF A NEW CRYSTAL FORM OF HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE, APE1, AND ITS IMPLICATIONS FOR THE CATALYTIC MECHANISM
Authors Beernink, P.T., Erzberger, J.P., Hadi, M.Z., Rupp, B., Segelke, B.W., Wilson III, D.M.
Method X-RAY DIFFRACTION
Structure factors resolution 2.2 rfactor 0.186 rfree 0.252
DPI 0.63 theoretical min: 0.26
Related PDB Entries 1HD7
Citations

The major human abasic endonuclease, Ape1, is an essential DNA repair enzyme that initiates the removal of apurinic/apyrimidinic sites from DNA, excises 3' replication-blocking moieties, and modulates the DNA binding activity of several transcriptional regulators. We have determined the X-ray structure of the full-length human Ape1 enzyme in two new crystal forms, one at neutral and one at acidic pH. The new structures are generally similar to the previously determined structure of a truncated Ape1 protein, but differ in the conformation of several loop regions and in spans of residues with weak electron density. While only one active-site metal ion is present in the structure determined at low pH, the structure determined from a crystal grown at the pH optimum of Ape1 nuclease activity, pH 7.5, has two metal ions bound 5 A apart in the active site. Enzyme kinetic data indicate that at least two metal-binding sites are functionally important, since Ca(2+) exhibits complex stimulatory and inhibitory effects on the Mg(2+)-dependent catalysis of Ape1, even though Ca(2+) itself does not serve as a cofactor. In conjunction, the structural and kinetic data suggest that Ape1 catalyzes hydrolysis of the DNA backbone through a two metal ion-mediated mechanism.

J.Mol.Biol. 2001 Apr; 307(4):1023- doi:10.1006/JMBI.2001.4529

Cross References
Database source Identifier Description
PubMed 11286553 JMOBAK
Biomolecule Structure Assembly Serial Assembly Type Conformational State Chains Ligands Atoms
1E9N/1 1E9N 1 monomer 0 1 2 1981
1E9N/2 1E9N 2 monomer 0 1 2 2019