6YRS

Structure of a new variant of GNCA ancestral beta-lactamase

Summary for 6YRS

• Entry DOI: 10.2210/pdb6yrs/pdb
• Descriptor: ancestral beta-lactamase, ACETATE ION, TRIETHYLENE GLYCOL, ... (7 entities in total)
• Functional Keywords: hydrolase, antibiotic resistance, ancestral reconstructed
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 59679.80

Authors

Gavira, J.A.,Risso, V.,Martinez-Rodriguez, S.,Sanchez-Ruiz, J.M.,Modi, T.,Ozkan, S.B. (deposition date: 2020-04-20, release date: 2021-03-03, Last modification date: 2024-01-24)

Primary citation

Modi, T.,Risso, V.A.,Martinez-Rodriguez, S.,Gavira, J.A.,Mebrat, M.D.,Van Horn, W.D.,Sanchez-Ruiz, J.M.,Banu Ozkan, S.
Hinge-shift mechanism as a protein design principle for the evolution of beta-lactamases from substrate promiscuity to specificity.
Nat Commun, 12:1852-1852, 2021

PubMed Abstract: TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian β-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site.

PubMed: 33767175
DOI: 10.1038/s41467-021-22089-0

Experimental method

X-RAY DIFFRACTION (1.7 Å)