6OVZ image
Deposition Date 2019-05-08
Release Date 2019-06-12
Last Version Date 2023-11-15
Entry Detail
PDB ID:
6OVZ
Keywords:
Title:
Crystal structure of the New Delhi metallo-beta-lactamase-1 adduct with a lysine-targeted affinity label
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
Resolution:
2.02 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Beta-lactamase
Gene (Uniprot):blaNDM-1
Chain IDs:A
Chain Length:235
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Beta-lactamase
Gene (Uniprot):blaNDM-1
Chain IDs:B
Chain Length:235
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
KCX B LYS modified residue
Primary Citation
A Lysine-Targeted Affinity Label for Serine-beta-Lactamase Also Covalently Modifies New Delhi Metallo-beta-lactamase-1 (NDM-1).
Biochemistry 58 2834 2843 (2019)
PMID: 31145588 DOI: 10.1021/acs.biochem.9b00393

Abstact

The divergent sequences, protein structures, and catalytic mechanisms of serine- and metallo-β-lactamases hamper the development of wide-spectrum β-lactamase inhibitors that can block both types of enzymes. The O-aryloxycarbonyl hydroxamate inactivators of Enterobacter cloacae P99 class C serine-β-lactamase are unusual covalent inhibitors in that they target both active-site Ser and Lys residues, resulting in a cross-link consisting of only two atoms. Many clinically relevant metallo-β-lactamases have an analogous active-site Lys residue used to bind β-lactam substrates, suggesting a common site to target with covalent inhibitors. Here, we demonstrate that an O-aryloxycarbonyl hydroxamate inactivator of serine-β-lactamases can also serve as a classical affinity label for New Delhi metallo-β-lactamase-1 (NDM-1). Rapid dilution assays, site-directed mutagenesis, and global kinetic fitting are used to map covalent modification at Lys211 and determine KI (140 μM) and kinact (0.045 min-1) values. Mass spectrometry of the intact protein and the use of ultraviolet photodissociation for extensive fragmentation confirm stoichiometric covalent labeling that occurs specifically at Lys211. A 2.0 Å resolution X-ray crystal structure of inactivated NDM-1 reveals that the covalent adduct is bound at the substrate-binding site but is not directly coordinated to the active-site zinc cluster. These results indicate that Lys-targeted affinity labels might be a successful strategy for developing compounds that can inactivate both serine- and metallo-β-lactamases.

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Primary Citation of related structures