1bss
From Proteopedia
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ECORV-T93A/DNA/CA2+
Overview
The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant, T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in, one of the active sites. One of these metals is ligated through an, inner-sphere water molecule to the phosphate group located 3' to the, scissile phosphate. A second inner-sphere water on this metal is, positioned approximately in-line for attack on the scissile phosphate., This structure corroborates the observation that the pro-SP phosphoryl, oxygen on the adjacent 3' phosphate cannot be modified without severe loss, of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI, endonucleases, suggests that ligation of a catalytic divalent metal ion to, this phosphate may occur in many type II restriction enzymes. Together, with previous cocrystal structures, these data allow construction of a, detailed model for the pretransition state configuration in EcoRV. This, model features three divalent metal ions per active site and invokes, assistance in the bond-making step by a conserved lysine, which stabilizes, the attacking hydroxide ion nucleophile.
About this Structure
1BSS is a Single protein structure of sequence from Escherichia coli with CA as ligand. Active as Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Full crystallographic information is available from OCA.
Reference
Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases., Horton NC, Newberry KJ, Perona JJ, Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13489-94. PMID:9811827
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