7KH9

Crystal structure of OXA-48 K73A in complex with imipenem

Summary for 7KH9

• Entry DOI: 10.2210/pdb7kh9/pdb
• Descriptor: Beta-lactamase, (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: beta-lactamase, carbapenemase, beta-lactamase inhibitor, complex, oxacillinase, hydrolase, hydrolase-hydrolase inhibitor complex
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 2
• Total formula weight: 57132.43

Authors

Palzkill, T.,Hu, L.,Sankaran, B.,Prasad, B.V.V. (deposition date: 2020-10-20, release date: 2021-02-10, Last modification date: 2023-10-18)

Primary citation

Stojanoski, V.,Hu, L.,Sankaran, B.,Wang, F.,Tao, P.,Prasad, B.V.V.,Palzkill, T.
Mechanistic Basis of OXA-48-like beta-Lactamases' Hydrolysis of Carbapenems.
Acs Infect Dis., 7:445-460, 2021

PubMed Abstract: Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are an important source of resistance to these last resort β-lactam antibiotics. OXA-48 is a member of a group of CHDLs named OXA-48-like enzymes. On the basis of sequence similarity, OXA-163 can be classified as an OXA-48-like enzyme, but it has altered substrate specificity. Compared to OXA-48, it shows impaired activity for carbapenems but displays an enhanced hydrolysis of oxyimino-cephalosporins. Here, we address the mechanistic and structural basis for carbapenem hydrolysis by OXA-48-like enzymes. Pre-steady-state kinetic analysis indicates that the rate-limiting step for OXA-48 and OXA-163 hydrolysis of carbapenems is deacylation and that the greatly reduced carbapenemase activity of OXA-163 compared to that of OXA-48 is due entirely to a slower deacylation reaction. Furthermore, our structural data indicate that the positioning of the β5-β6 loop is necessary for carbapenem hydrolysis by OXA-48. A major difference between the OXA-48 and OXA-163 complexes with carbapenems is that the 214-RIEP-217 deletion in OXA-163 creates a large opening in the active site that is absent in the OXA-48/carbapenem structures. We propose that the larger active site results in less constraint on the conformation of the 6α-hydroxyethyl group in the acyl-enzyme. The acyl-enzyme intermediate assumes multiple conformations, most of which are incompatible with rapid deacylation. Consistent with this hypothesis, molecular dynamics simulations indicate that the most stable complex is formed between OXA-48 and imipenem, which correlates with the OXA-48 hydrolysis of imipenem being the fastest observed. Furthermore, the OXA-163 complexes with imipenem and meropenem are the least stable and show significant conformational fluctuations, which correlates with the slow hydrolysis of these substrates.

PubMed: 33492952
DOI: 10.1021/acsinfecdis.0c00798

Experimental method

X-RAY DIFFRACTION (2.29 Å)