1h56

From Proteopedia

Revision as of 14:23, 5 November 2007

STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF A NEW MAGNESIUM ION BINDING SITE NEAR TYR94 IN THE RESTRICTION ENDONUCLEASE PVUII

Overview

We have determined the crystal structure of the PvuII endonuclease in the, presence of Mg(2+). According to the structural data, divalent metal ion, binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+), complex has two distinct metal ion binding sites, one in each monomer. One, site is formed by the catalytic residues Asp58 and Glu68, and has, extensive similarities to a catalytically important site found in all, structurally examined restriction endonucleases. The other binding site is, located in the other monomer, in the immediate vicinity of the hydroxyl, group of Tyr94; it has no analogy to metal ion binding sites found so far, in restriction endonucleases. To assign the number of metal ions involved, and to better understand the role of Mg(2+) binding to Tyr94 for the, function of PvuII, we have exchanged Tyr94 by Phe and characterized the, metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F, variant. Wild-type PvuII cleaves both strands of the DNA in a concerted, reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA, cleavage, occurs with a Hill coefficient of 4, meaning that at least two, metal ions are bound to each subunit in a cooperative fashion upon, formation of the active complex. Quenched-flow experiments show that DNA, cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with, enzyme or DNA than if preformed enzyme-DNA complexes are mixed with, Mg(2+). These results show that Mg(2+) cannot easily enter the active, center of the preformed enzyme-DNA complex, but that for fast cleavage the, metal ions must already be bound to the apoenzyme and carried with the, enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to, wild-type PvuII, does not cleave DNA in a concerted manner and metal ion, binding occurs with a Hill coefficient of 1. These results indicate that, removal of the Mg(2+) binding site at Tyr94 completely disrupts the, cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F, cleaves DNA about ten times more slowly than wild-type PvuII, regardless, of the order of mixing. From these results we conclude that wild-type, PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+), required for catalysis are already bound at the enzyme, one of them at, Tyr94. We suggest that this Mg(2+) is shifted to the active center during, binding of a specific DNA substrate. These results, for the first time, shed light on the pathway by which metal ions as essential cofactors enter, the catalytic center of restriction endonucleases.

About this Structure

1H56 is a Single protein structure of sequence from Proteus vulgaris with MG as ligand. Active as Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Structure known Active Site: MGA. Full crystallographic information is available from OCA.

Reference

Structural and biochemical characterization of a new Mg(2+) binding site near Tyr94 in the restriction endonuclease PvuII., Spyridaki A, Matzen C, Lanio T, Jeltsch A, Simoncsits A, Athanasiadis A, Scheuring-Vanamee E, Kokkinidis M, Pingoud A, J Mol Biol. 2003 Aug 8;331(2):395-406. PMID:12888347

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