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PDBsum entry 1xhu

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Top Page protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
1xhu
Jmol
Contents
Protein chains
257 a.a.
DNA/RNA
Waters ×559

References listed in PDB file
Key reference
Title Mechanistic insights from the structures of hincii bound to cognate DNA cleaved from addition of mg2+ and mn2+.
Authors C.Etzkorn, N.C.Horton.
Ref. J Mol Biol, 2004, 343, 833-849. [DOI no: 10.1016/j.jmb.2004.08.082]
PubMed id 15476804
Abstract
The three-dimensional X-ray crystal structures of HincII bound to cognate DNA containing GTCGAC and Mn(2+) or Mg(2+), at 2.50A and 2.95A resolution, respectively, are presented. In both structures, the DNA is found cleaved, and the positions of the active-site groups, cleaved phosphate group, and 3' oxygen atom of the leaving group are in very similar positions. Two highly occupied Mn(2+) positions are found in each active site of the four crystallographically independent subunit copies in the HincII/DNA/Mn(2+) structure. The manganese ion closest to the previously identified single Ca(2+) position of HincII is shifted 1.7A and has lost direct ligation to the active-site aspartate residue, Asp127. A Mn(2+)-ligated water molecule in a position analogous to that seen in the HincII/DNA/Ca(2+) structure, and proposed to be the attacking nucleophile, is beyond hydrogen bonding distance from the active-site lysine residue, Lys129, but remains within hydrogen bonding distance from the proRp oxygen atom of the phosphate group 3' to the scissile phosphate group. In addition, the position of the cleaved phosphate group is on the opposite side of the axis connecting the two metal ions relative to that found in the BamHI/product DNA/Mn(2+) structure. Mechanistic implications are discussed, and a model for the two-metal-ion mechanism of DNA cleavage by HincII is proposed.
Figure 2.
Figure 2. (a) Geometry around the two main manganese ions. (b) Simulated annealing omit map at the 3s level of the HincII/DNA/Mn 2C structure subunit A where the nucleotides around the scissile bond, Cyt7 and Gua8, have been excluded. The manganese ions are shown as green spheres. (c) Simulated annealing omit map at the 3s level of the HincII/DNA/Mg 2C structure subunit A where the nucleotides around the scissile bond, Cyt7 and Gua8, have been excluded. Water molecules are shown as small red spheres. (d) Superposition of subunit A of HincII/cleaved DNA/Mn 2C (red) and HincII/cleaved DNA/Mg 2C (green) showing an equivalent position of the phosphate resulting from cleavage. Although both of the two main Mn 2C positions (large red sphere) were present in the Figure, only one is visible, as the view is down the Mn 2C --Mn 2C axis. Water molecules are indicated by small spheres.
The above figure is reprinted by permission from Elsevier: J Mol Biol (2004, 343, 833-849) copyright 2004.
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