Structural Insights into Substrate Recognition by a Colistin Resistance Enzyme

Antimicrobial resistance is a serious and growing threat affecting the medical system.  The over-use and misuse of antibiotics, along with natural properties of bacteria, such as a capacity to exchange antibiotic genes, has resulted in the current situation where every class of approved antibiotic is threatened by resistance.

Bacteria possess multiple mechanisms of resisting the action of antibiotics, including efflux pumps that eject antibiotics from the interior of cells, enzyme-catalyzed chemical modification of the drug, or modification of the cellular drug target. In 2016, a gene, mcr-1, was discovered in E. coli bacteria in China that confers resistance to polymyxin antibiotics, including colistin, which are considered important “last resort” drugs when frontline therapies fail. Since then, this gene and its closely related family members have been discovered worldwide and in multiple species that cause difficult infections such as Klebsiella pneumoniae, Salmonella enterica and Enterobacter cloacae. It is thought that mcr-1 and its family members alter the cellular target of polymyxin antibiotics, lipid A, through modification with phosphoethanolamine donated by the membrane lipid phosphatidylethanolamine. This modification renders polymyxins less effective.

To understand this and other types of emerging mechanisms of antibiotic resistance, researchers from the Center for Structural Genomics of Infectious Diseases (CSGID) and collaborators at the University of Calgary and the University of Toronto, are conducting structural genomics studies into mechanisms of antimicrobial resistance. Their work has provided key molecular details into this form of colistin resistance. The research team determined the crystal structure of the catalytic domain of a mcr-1 family member, called ICRMc, from the bacteria Moraxella catarrhalis. This crystal structure was solved with a fragment of one of the enzyme’s substrates, phosphoethanolamine. The crystal structure of ICRMc resolved key active site features, including a cavity for binding substrates, zinc binding sites, and the active site residues responsible for catalysis and phosphate recognition. Mutational analysis verified these as essential amino acids for polymyxin resistance by ICRMc. The structure also showed that all phosphoethanolamine family members conserve these amino acids, meaning the structure provides general insights into the broader family.

The next steps in this research are to elucidate the structure and function of the full-length enzyme with its transmembrane domain intact, and to identify and characterize small molecule inhibitors that would block the function of phosphoethanolamine family members. Such a combination approach is increasingly used in the clinic; these ICRMc inhibitory compounds could be complemented with polymyxins to ensure this form of antibiotic resistance is addressed. Crystal structures of antibiotic resistance enzymes such as this structure of the catalytic domain of ICRMc will be essential for this work.

Reference: Stogios PJ, Cox G2 Zubyk HL, Evdokimova E, Wawrzak Z, Wright GD, Savchenko A (2018) Substrate Recognition by a Colistin Resistance Enzyme from Moraxella catarrhalis ACS Chemical Biology 13:1322.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197822/

Coordinates are available in the Protein Data Bank (www.rcsb.org) PDB IDs: 6BNE, 6BNF, 6BNC, 6BND





Refer to caption for description

NIAID-supported researchers determined the crystal structure of the catalytic domain of a mcr-1 family member, called ICRMc, from the bacteria Moraxella catarrhalis.

Credit
CSGID

NIAID-supported researchers determined the crystal structure of the catalytic domain of a mcr-1 family member, called ICRMc, from the bacteria Moraxella catarrhalis.

Credit:
CSGID
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