Jawed Ahmed, Aakansha Chaudhary, Manisha Mittal, Mohaddeseh Mousavi
Department of Computer Science, Jamia Hamdard, New Delhi-110062, India.

ABSTRACT

Recently determined crystal structure of type II restriction endonucleases has produced a plethora of information on the basis for target site sequence selectivity. The positioning and role of metal ions in DNA recognition sites might reflect important properties of proteins -DNA interaction. Although acidic n basic groups in the active sites can be identified and in some cases divalent metal binding sites delineated a convincing picture clarifying the way in which the attacking hydroxide ion is generated.We have examined the interatomic distances between metal ions and proposed key catalytic residues in the binding sites of several type II restriction endonuclease. After retrieving their crystal structures from REBASE, the enzyme used for this study have been categorised on the basis of the number of metal ions identified in their crystal structures using tools such as REBASE restriction enzyme database,protein databank,fasta format,(PS)2 server and ligand explorer.Among the experimentaly characterized type II restriction endonucleases, whose apparently full length sequences are available in REBASE, they are categorised to follow either the single, two, three, four or the six metal ion mechanism. Read more…