1tx3
From Proteopedia
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HINCII BOUND TO COGNATE DNA
Overview
The 2.8 A crystal structure of the type II restriction endonuclease HincII, bound to Ca(2+) and cognate DNA containing GTCGAC is presented. The DNA is, uncleaved, and one calcium ion is bound per active site, in a position, previously described as site I in the related blunt cutting type II, restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and, Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494], as well as that found in other related enzymes. Unlike the site I metal in, EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the, observed calcium cation is directly ligated to the pro-S(p) oxygen of the, scissile phosphate. A calcium ion-ligated water molecule is well, positioned to act as the nucleophile in the phosphodiester bond cleavage, reaction, and is within hydrogen bonding distance of the conserved active, site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate, group 3' of the scissile phosphate, suggesting possible roles for these, groups in the catalytic mechanism. Kinetic data consistent with an, important role for the 3'-phosphate group in DNA cleavage by HincII are, presented. The previously observed sodium ion [Horton, N. C., Dorner, L., F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the, active sites of the Ca(2+)-bound structure; however, kinetic data show, little effect on the single-turnover rate of DNA cleavage in the absence, of Na(+) ions.
About this Structure
1TX3 is a Single protein structure of sequence from Haemophilus influenzae with NA as ligand. Active as Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Full crystallographic information is available from OCA.
Reference
Ca2+ binding in the active site of HincII: implications for the catalytic mechanism., Etzkorn C, Horton NC, Biochemistry. 2004 Oct 26;43(42):13256-70. PMID:15491133
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