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The structure of the zinc-dependent beta-lactamase II from Bacillus cereus has
been determined at 1.9 A resolution in a crystal form with two molecules in the
asymmetric unit and 400 waters (space group P3121; Rcryst = 20.8%). The active
site contains two zinc ions: Zn1 is tightly coordinated by His86, His88, and
His149, while Zn2 is loosely coordinated by Asp90, Cys168, and His210. A water
molecule (W1) lies between the two zinc ions but is significantly closer to Zn1
and at a distance of only 1.9 A is effectively a hydroxide moiety and a
potential, preactivated nucleophile. In fact, Asp90 bridges W1 to Zn2, and its
location is thus distinct from that of the bridging water molecules in the
binuclear zinc peptidases or other binuclear zinc hydrolases. Modeling of
penicillin, cephalosporin, and carbapenem binding shows that all are readily
accommodated within the shallow active site cleft of the enzyme, and the
Zn1-bound hydroxide is ideally located for nucleophilic attack at the
beta-lactam carbonyl. This enzyme also functions with only one zinc ion present.
The Zn1-Zn2 distances differ in the two independent molecules in the crystal
(3.9 and 4.4 A), yet the Zn1-W1 distances are both 1.9 A, arguing against
involvement of Zn2 in W1 activation. The role of Zn2 is unclear, but the B.
cereus enzyme may be an evolutionary intermediate between the mono- and bizinc
metallo-beta-lactamases. The broad specificity of this enzyme, together with the
increasing prevalence of zinc-dependent metallo-beta-lactamases, poses a real
clinical threat, and this structure provides a basis for understanding its
mechanism and designing inhibitors.
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