4S2M

Crystal Structure of OXA-163 complexed with iodide in the active site

Summary for 4S2M

• Entry DOI: 10.2210/pdb4s2m/pdb
• Related: 4S2L
• Descriptor: Beta-lactamase, IODIDE ION (3 entities in total)
• Functional Keywords: globular, hydrolase
• Biological source: Enterobacter cloacae
• Total number of polymer chains: 4
• Total formula weight: 112366.41

Authors

Stojanoski, V.,Hu, L.,Palzkill, T.G.,Prasad, B. (deposition date: 2015-01-21, release date: 2015-07-22, Last modification date: 2023-09-20)

Primary citation

Stojanoski, V.,Chow, D.C.,Fryszczyn, B.,Hu, L.,Nordmann, P.,Poirel, L.,Sankaran, B.,Prasad, B.V.,Palzkill, T.
Structural Basis for Different Substrate Profiles of Two Closely Related Class D beta-Lactamases and Their Inhibition by Halogens.
Biochemistry, 54:3370-3380, 2015

PubMed Abstract: OXA-163 and OXA-48 are closely related class D β-lactamases that exhibit different substrate profiles. OXA-163 hydrolyzes oxyimino-cephalosporins, particularly ceftazidime, while OXA-48 prefers carbapenem substrates. OXA-163 differs from OXA-48 by one substitution (S212D) in the active-site β5 strand and a four-amino acid deletion (214-RIEP-217) in the loop connecting the β5 and β6 strands. Although the structure of OXA-48 has been determined, the structure of OXA-163 is unknown. To further understand the basis for their different substrate specificities, we performed enzyme kinetic analysis, inhibition assays, X-ray crystallography, and molecular modeling. The results confirm the carbapenemase nature of OXA-48 and the ability of OXA-163 to hydrolyze the oxyimino-cephalosporin ceftazidime. The crystal structure of OXA-163 determined at 1.72 Å resolution reveals an expanded active site compared to that of OXA-48, which allows the bulky substrate ceftazidime to be accommodated. The structural differences with OXA-48, which cannot hydrolyze ceftazidime, provide a rationale for the change in substrate specificity between the enzymes. OXA-163 also crystallized under another condition that included iodide. The crystal structure determined at 2.87 Å resolution revealed iodide in the active site accompanied by several significant conformational changes, including a distortion of the β5 strand, decarboxylation of Lys73, and distortion of the substrate-binding site. Further studies showed that both OXA-163 and OXA-48 are inhibited in the presence of iodide. In addition, OXA-10, which is not a member of the OXA-48-like family, is also inhibited by iodide. These findings provide a molecular basis for the hydrolysis of ceftazidime by OXA-163 and, more broadly, show how minor sequence changes can profoundly alter the active-site configuration and thereby affect the substrate profile of an enzyme.

PubMed: 25938261
DOI: 10.1021/acs.biochem.5b00298

Experimental method

X-RAY DIFFRACTION (2.87 Å)