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Figure 5.
Figure 5. DNA Recognition
(Top) Schematic
representation of DNA contacts for BglII (left), BstYI (middle),
and BamHI (right). Two-fold symmetry is assumed for all three
enzymes. The DNA recognition sequences are highlighted in
yellow; with major and minor groove contacts indicated as red
and blue lines, respectively. Contacts to the phosphate backbone
(purple) are also displayed for BstYI (green). In the BstYI
complex, only two residues (Ser172 and Lys133) mediate
recognition of the core base pairs and, unlike BamHI and BglII,
there is a direct contact to an adenine of a flanking A:T base
pair, via Tyr115.
(Bottom) Close-up view of protein-DNA
contacts in one half-site of the recognition sequence. DNA bases
are colored in yellow and water molecules are colored cyan.
Hydrogen bonding is indicated by dashed lines (white). In the
BstYI-DNA complex, Ser172 forms a hydrogen bond to the middle
cytosine, identical to Asn140 in BglII and Asp154 in BamHI.
However, Gly173 does not specify the outer base pair, like the
equivalent residues in BglII (Ser141) and BamHI (Arg155).
Instead, a cavity between the glycine and the nucleotide allows
for water-mediated recognition of N7 of the outer purine by a
lysine (Lys133). This lysine residue also forms bidentate
hydrogen bonds with the middle guanine and VDW contacts with the
inner thymine.
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