1E9N

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

Summary for 1E9N

• Entry DOI: 10.2210/pdb1e9n/pdb
• Related: 1BIX 1CQG 1CQH
• Descriptor: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, LEAD (II) ION (3 entities in total)
• Functional Keywords: dna repair, dna repair endonuclease, base excision repair, abasic endonuclease, ape1, hap1, ref-1, alpha, beta sandwich
• Biological source: HOMO SAPIENS (HUMAN)
• Total number of polymer chains: 2
• Total formula weight: 72041.78

Authors

Beernink, P.T.,Segelke, B.W.,Rupp, B. (deposition date: 2000-10-24, release date: 2001-02-16, Last modification date: 2024-11-06)

Primary citation

Beernink, P.T.,Segelke, B.W.,Hadi, M.Z.,Erzberger, J.P.,Wilson III, D.M.,Rupp, B.
Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
J.Mol.Biol., 307:1023-, 2001

PubMed Abstract: 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.

PubMed: 11286553
DOI: 10.1006/JMBI.2001.4529

Experimental method

X-RAY DIFFRACTION (2.2 Å)