X-ray Structure of the ZnII β-Lactamase from Bacteroides fragilis in an Orthorhombic Crystal Form

Abstract

β-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to β-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-β-lactamase from Bacillus cereus, has been solved at 2.5 Å resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914–4921]. Recently, the crystal structure of the metallo-β-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823–836]. The structure of the metallo-β-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 Å resolution is reported here. The final crystallographic R is 0.196 for all the 32 501 observed reflections in the range 10–2.0 Å. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-β-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.