Pfam PF02923: Restriction endonuclease BamHI (domain)
This entry represents BamHI restriction endonucleases, which recognises the DNA sequence GGATCC and cleaves after G-1 . The enzyme binds as a dimer to the symmetrical GGATCC sequence but it recognises this sequence in an asymmetric manner, in which the C-terminal arm of one BamHI subunit goes into the DNA minor groove while the corresponding region of the other subunit follows the DNA sugar-phosphate backbone . The BamHI structure consists of a central mixed Î² -sheet with Î±-helices packed on both sides.

This entry also represents the Type II restriction enzyme OkrAI that is isoschizomer of BamHI . OkrAI is a minimal version of BamHI, lacking the N- and C-terminal helices as well as the internal 3(10) helix of BamHI. Despite these structural differences, OkrAI recognises the DNA in a remarkably similar manner to BamHI .
There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:


 * Type I enzymes (3.1.21.3) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72) activities.
 * Type II enzymes (3.1.21.4) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
 * Type III enzymes (3.1.21.5) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72).
 * Type IV enzymes target methylated DNA.

Type II restriction endonucleases (3.1.21.4) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four Î²-strands and one Î±-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .
Wikipedia: BamHI is a type II restriction endonuclease, having the capacity for recognizing short sequences of DNA and specifically cleaving them at a target site. This exhibit focuses on the structure-function relations of BamHI as described by Newman, et al. (1995). BamHI binds at the recognition sequence 5'-GGATCC-3', and cleaves these sequences just after the 5'-guanine on each strand. This cleavage results in sticky ends which are 4 bp long. In its unbound form, BamHI displays a central b sheet, which resides in between α-helices.