1N9B

Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme

Summary for 1N9B

• Entry DOI: 10.2210/pdb1n9b/pdb
• Related: 1HTZ 1SHV
• Descriptor: BETA-LACTAMASE SHV-2, CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (5 entities in total)
• Functional Keywords: beta-lactam hydrolase, penicillinase, detergent binding, drug design, radiation damage, hydrolase
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 30310.72

Authors

Nukaga, M.,Mayama, K.,Hujer, A.M.,Bonomo, R.A.,Knox, J.R. (deposition date: 2002-11-22, release date: 2003-04-08, Last modification date: 2024-11-06)

Primary citation

Nukaga, M.,Mayama, K.,Hujer, A.M.,Bonomo, R.A.,Knox, J.R.
Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme
J.Mol.Biol., 328:289-301, 2003

PubMed Abstract: Bacterial beta-lactamases hydrolyze beta-lactam antibiotics such as penicillins and cephalosporins. The TEM-type class A beta-lactamase SHV-2 is a natural variant that exhibits activity against third-generation cephalosporins normally resistant to hydrolysis by class A enzymes. SHV-2 contains a single Gly238Ser change relative to the wild-type enzyme SHV-1. Crystallographic refinement of a model including hydrogen atoms gave R and R(free) of 12.4% and 15.0% for data to 0.91 A resolution. The hydrogen atom on the O(gamma) atom of the reactive Ser70 is clearly seen for the first time, bridging to the water molecule activated by Glu166. Though hydrogen atoms on the nearby Lys73 are not seen, this observation of the Ser70 hydrogen atom and the hydrogen bonding pattern around Lys73 indicate that Lys73 is protonated. These findings support a role for the Glu166-water couple, rather than Lys73, as the general base in the deprotonation of Ser70 in the acylation process of class A beta-lactamases. Overlay of SHV-2 with SHV-1 shows a significant 1-3 A displacement in the 238-242 beta-strand-turn segment, making the beta-lactam binding site more open to newer cephalosporins with large C7 substituents and thereby expanding the substrate spectrum of the variant enzyme. The OH group of the buried Ser238 side-chain hydrogen bonds to the main-chain CO of Asn170 on the Omega loop, that is unaltered in position relative to SHV-1. This structural role for Ser238 in protein-protein binding makes less likely its hydrogen bonding to oximino cephalosporins such as cefotaxime or ceftazidime.

PubMed: 12684014
DOI: 10.1016/S0022-2836(03)00210-9

Experimental method

X-RAY DIFFRACTION (0.9 Å)