5A91

15K X-ray ligand free: Exploring the Mechanism of beta-Lactam Ring Protonation in the Class A beta-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

Summary for 5A91

• Entry DOI: 10.2210/pdb5a91/pdb
• Related: 5A90 5A92 5A93
• Descriptor: Beta-lactamase Toho-1, SULFATE ION (3 entities in total)
• Functional Keywords: hydrolase, beta lactamase, neutron crystallography
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 28598.07

Authors

Vandavasi, V.G.,Weiss, K.L.,Cooper, J.B.,Erskine, P.T.,Tomanicek, S.J.,Ostermann, A.,Schrader, T.E.,Ginell, S.L.,Coates, L. (deposition date: 2015-07-17, release date: 2015-12-16, Last modification date: 2024-05-08)

Primary citation

Vandavasi, V.G.,Weiss, K.L.,Cooper, J.B.,Erskine, P.T.,Tomanicek, S.J.,Ostermann, A.,Schrader, T.E.,Ginell, S.L.,Coates, L.
Exploring the Mechanism of Beta-Lactam Ring Protonation in the Class a Beta-Lactamase Acylation Mechanism Using Neutron and X-Ray Crystallography.
J.Med.Chem., 59:474-, 2016

PubMed Abstract: The catalytic mechanism of class A β-lactamases is often debated due in part to the large number of amino acids that interact with bound β-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type β-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 β-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzyme's native machinery.

PubMed: 26630115
DOI: 10.1021/ACS.JMEDCHEM.5B01215

Experimental method

X-RAY DIFFRACTION (1.2 Å)