1e9n

From Proteopedia

Revision as of 14:03, 5 November 2007

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

Overview

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.

About this Structure

1E9N is a Single protein structure of sequence from Homo sapiens with PB as ligand. Active as DNA-(apurinic or apyrimidinic site) lyase, with EC number 4.2.99.18 Structure known Active Sites: PB1, PB2, PB3 and PB4. Full crystallographic information is available from OCA.

Reference

Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism., Beernink PT, Segelke BW, Hadi MZ, Erzberger JP, Wilson DM 3rd, Rupp B, J Mol Biol. 2001 Apr 6;307(4):1023-34. PMID:11286553

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