8EO5

Crystal structure of the class A beta-lactamase precursor LRA-5 from an Alaskan soil metagenome at 1.8 Angstrom resolution

Summary for 8EO5

• Entry DOI: 10.2210/pdb8eo5/pdb
• Descriptor: LRA-5, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (3 entities in total)
• Functional Keywords: beta-lactamase precursor, environmental resistome, soil metagenome, antimicrobial protein
• Biological source: uncultured soil bacterium
• Total number of polymer chains: 2
• Total formula weight: 62076.96

Authors

Power, P.,D'Amico Gonzalez, G.,Centron, D.,Gutkind, G.,Handelsman, J.,Klinke, S. (deposition date: 2022-10-02, release date: 2023-09-06, Last modification date: 2026-05-13)

Primary citation

D'Amico Gonzalez, G.,Rodriguez, M.M.,Penzotti, P.,Brunetti, F.,Ghiglione, B.,Moe, L.A.,Centron, D.,Gutkind, G.,Gao, L.,Haider, S.,Powers, R.A.,Klinke, S.,Power, P.
Proposal of metagenomic-origin LRA-5 as a precursor of active beta-lactamases through Tyr69Gln and Val166Glu amino acid substitutions: a functional and structural analysis.
Antimicrob.Agents Chemother., 70:e0067525-e0067525, 2026

PubMed Abstract: Wild-type LRA-5, recovered from Alaskan soil samples, shares no more than 33% amino acid sequence identity with enzymes from pathogens like PER β-lactamases. Recombinant expressing wild-type LRA-5 and its engineered variants LRA-5 and LRA-5 showed MIC values equivalent to control strains. However, LRA-5 displayed MICs above the resistant breakpoint for some β-lactams. Kinetic parameters correlated with the MICs, showing that the catalytic efficiency of LRA-5 was comparable to those from class A β-lactamases, such as CTX-M-15, PER-2, and KPC-2. LRA-5 exhibited / values up to 11,000-fold higher compared to wild-type LRA-5, which is associated with the presence of Glu166. The X-ray crystallographic structure of wild-type LRA-5 (1.80 Å; PDB 8EO5) shows that the lack of both Glu166 and a deacylation water molecule contributes to a biologically insignificant activity. Interactions observed between LRA-5 and ceftazidime (2.35 Å; PDB 8EO6) show structural conservation with other β-lactamases. In contrast, the crystallographic structure of LRA-5 (2.15 Å; PDB 8EO7) bears a deacylation water molecule that is associated with the increase in catalytic activity compared to the wild-type variant. Circular dichroism results confirm that amino acid substitutions in LRA-5 do not affect the overall content of the secondary/tertiary structures. Evidence suggests that alternative evolutionary paths could have occurred for β-lactamases like LRA-5, produced by environmental microorganisms: (i) proteins having similar structural features than active β-lactamases may accumulate a small number of mutations (e.g., Y69Q/V166E) to yield active enzymes and (ii) the β-lactamase fold may have lost key residues in the absence of antibiotics.

PubMed: 41312992
DOI: 10.1128/aac.00675-25

Experimental method

X-RAY DIFFRACTION (1.8 Å)