Crystal structure of the zinc-dependent β-lactamase from Bacillus cereus at 1.9 Å resolution:: Binuclear active site with features of a mononuclear enzyme
Crystal structure of the zinc-dependent β-lactamase from Bacillus cereus at 1.9 Å resolution:: Binuclear active site with features of a mononuclear enzyme
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DOI：
10.1021/bi980506i
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发表时间：
1998-09-08
期刊：
影响因子：
2.9
通讯作者：
Sutton, BJ
中科院分区：
文献类型：
--
作者：
Fabiane, SM;Sohi, MK;Sutton, BJ
来自蜡状芽孢杆菌的锌依赖性β-内酰胺酶II的结构已在1.9埃分辨率下以晶体形式确定，该晶体形式在不对称单元中具有两个分子和400个沃茨（空间群P3（1）21; R-cryst = 20.8%）。活性位点含有两个锌离子：Zn 1与His 86、His 88和His 149紧密配位，而Zn 2与Asp 90、Cys 168和His 210松散配位。水分子（W1）位于两个锌离子之间，但明显更接近Zn 1，并且在仅1.9埃的距离处有效地是氢氧化物部分和潜在的预活化亲核试剂。事实上，Asp 90桥W1锌？因此它的位置不同于双核锌肽酶或其它双核锌水解酶中的桥接水分子。青霉素，头孢菌素和碳青霉烯结合的建模表明，所有的都很容易容纳在浅活性位点裂缝的酶，和锌1结合的氢氧化物是理想的位于亲核攻击的β-内酰胺羰基。这种酶也仅在存在一个锌离子的情况下起作用。晶体中两个独立分子的Zn 1-Zn 2距离不同（3.9和4.4埃），但Zn 1-W1距离均为1.9埃，这与Zn 2参与W1活化有关。Zn 2的作用尚不清楚，但B.蜡状酶可能是单金属β-内酰胺酶和双金属β-内酰胺酶之间的进化中间体。这种酶的广泛特异性，以及锌依赖性金属β-内酰胺酶的日益流行，构成了真实的临床威胁，这种结构为理解其机制和设计抑制剂提供了基础。
The structure of the zinc-dependent beta-lactamase II from Bacillus cereus has been determined at 1.9 Angstrom resolution in a crystal form with two molecules in the asymmetric unit and 400 waters (space group P3(1)21; R-cryst = 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 Angstrom is effectively a hydroxide moiety and a potential, preactivated nucleophile. In fact, Asp90 bridges W1 to Zn? and its location is thus distinct from that nf 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 Angstrom), yet the Zn1-W1 distances are both 1.9 Angstrom, 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.