1dc1
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(New page: 200px<br /><applet load="1dc1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dc1, resolution 1.70Å" /> '''RESTRICTION ENZYME B...)
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Revision as of 11:02, 20 November 2007
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RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD
Overview
BACKGROUND: Restriction endonucleases form a diverse family of proteins, with substantial variation in sequence, structure, and interaction with, recognition site DNA. BsoBI is a thermophilic restriction endonuclease, that exhibits both base-specific and degenerate recognition within the, sequence CPyCGPuG. RESULTS: The structure of BsoBI complexed to cognate, DNA has been determined to 1.7 A resolution, revealing several, unprecedented features. Each BsoBI monomer is formed by inserting a, helical domain into an expanded EcoRI-type catalytic domain. DNA is, completely encircled by a BsoBI dimer. Recognition sequence DNA lies, within a 20 A long tunnel of protein that excludes bulk solvent., Interactions with the specific bases are made in both grooves through, direct and water-mediated hydrogen bonding. Interaction with the, degenerate position is mediated by a purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the purine N6/O6 and, pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active, site residues of the DX(n)(E/D)ZK restriction enzyme motif, His253 is, positioned to act as a general base. CONCLUSIONS: A catalytic mechanism, employing His253 and two metal ions is proposed. If confirmed, this would, be the first example of histidine-mediated catalysis in a restriction, endonuclease. The structure also provides two novel examples of the role, of water in protein-DNA interaction. Degenerate recognition may be, mediated by employing water as a hydrogen bond donor or acceptor. The, structure of DNA in the tunnel may also be influenced by the absence of, bulk solvent.
About this Structure
1DC1 is a Single protein structure of sequence from Geobacillus stearothermophilus with DIO as ligand. Active as Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Full crystallographic information is available from OCA.
Reference
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis., van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM, Structure. 2001 Feb 7;9(2):133-44. PMID:11250198
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