7WZU

Crystal structure of metallo-beta-lactamase IMP-6.

Summary for 7WZU

• Entry DOI: 10.2210/pdb7wzu/pdb
• Descriptor: Beta-lactamase, ZINC ION (3 entities in total)
• Functional Keywords: metallo-beta-lactamase, zinc(ii) ion, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 100989.86

Authors

Yamaguchi, Y.,Kurosaki, H. (deposition date: 2022-02-19, release date: 2023-01-04, Last modification date: 2023-11-29)

Primary citation

Yamaguchi, Y.,Kato, K.,Ichimaru, Y.,Uenosono, Y.,Tawara, S.,Ito, R.,Matsuse, N.,Wachino, J.I.,Toma-Fukai, S.,Jin, W.,Arakawa, Y.,Otsuka, M.,Fujita, M.,Fukuishi, N.,Sugiura, K.,Imai, M.,Kurosaki, H.
Difference in the Inhibitory Effect of Thiol Compounds and Demetallation Rates from the Zn(II) Active Site of Metallo-beta-lactamases (IMP-1 and IMP-6) Associated with a Single Amino Acid Substitution.
Acs Infect Dis., 9:65-78, 2023

PubMed Abstract: Gram-negative bacteria producing metallo-β-lactamases (MBLs) have become a considerable threat to public health. MBLs including the IMP, VIM, and NDM types are Zn(II) enzymes that hydrolyze the β-lactam ring present in a broad range of antibiotics, such as -benzylpenicillin, meropenem, and imipenem. Among IMPs, IMP-1 and IMP-6 differ in a single amino acid substitution at position 262, where serine in IMP-1 is replaced by glycine in IMP-6, conferring a change in substrate specificity. To investigate how this mutation influences enzyme function, we examined lactamase inhibition by thiol compounds. Ethyl 3-mercaptopropionate acted as a competitive inhibitor of IMP-1, but a noncompetitive inhibitor of IMP-6. A comparison of the crystal structures previously reported for IMP-1 (PDB code: 5EV6) and IMP-6 (PDB code: 6LVJ) revealed a hydrogen bond between the side chain of Ser262 and Cys221 in IMP-1 but the absence of hydrogen bond in IMP-6, which affects the Zn2 coordination sphere in its active site. We investigated the demetallation rates of IMP-1 and IMP-6 in the presence of chelating agent ethylenediaminetetraacetic acid (EDTA) and found that the demetallation reactions had fast and slow phases with a first-order rate constant ( = 1.76 h, = 0.108 h for IMP-1, and = 14.0 h and = 1.66 h for IMP-6). The difference in the flexibility of the Zn2 coordination sphere between IMP-1 and IMP-6 may influence the demetallation rate, the catalytic efficiency against β-lactam antibiotics, and the inhibitory effect of thiol compounds.

PubMed: 36519431
DOI: 10.1021/acsinfecdis.2c00395

Experimental method

X-RAY DIFFRACTION (1.954 Å)