2FFY

AmpC beta-lactamase N289A mutant in complex with a boronic acid deacylation transition state analog compound SM3

Summary for 2FFY

• Entry DOI: 10.2210/pdb2ffy/pdb
• Related: 1PI4
• Descriptor: Beta-lactamase, POTASSIUM ION, (1R)-1-(2-THIENYLACETYLAMINO)-1-PHENYLMETHYLBORONIC ACID, ... (5 entities in total)
• Functional Keywords: ampc; beta-lactamase; deacylation; transition state; boronic acid, hydrolase
• Biological source: Escherichia coli
• Cellular location: Periplasm: P00811
• Total number of polymer chains: 2
• Total formula weight: 79813.23

Authors

Chen, Y.,Minasov, G.,Roth, T.A.,Prati, F.,Shoichet, B.K. (deposition date: 2005-12-20, release date: 2006-03-28, Last modification date: 2024-11-20)

Primary citation

Chen, Y.,Minasov, G.,Roth, T.A.,Prati, F.,Shoichet, B.K.
The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution
J.Am.Chem.Soc., 128:2970-2976, 2006

PubMed Abstract: Beta-lactamases confer bacterial resistance to beta-lactam antibiotics, such as penicillins. The characteristic class C beta-lactamase AmpC catalyzes the reaction with several key residues including Ser64, Tyr150, and Lys67. Here, we describe a 1.07 A X-ray crystallographic structure of AmpC beta-lactamase in complex with a boronic acid deacylation transition-state analogue. The high quality of the electron density map allows the determination of many proton positions. The proton on the Tyr150 hydroxyl group is clearly visible and is donated to the boronic oxygen mimicking the deacylation water. Meanwhile, Lys67 hydrogen bonds with Ser64Ogamma, Asn152Odelta1, and the backbone oxygen of Ala220. This suggests that this residue is positively charged and has relinquished the hydrogen bond with Tyr150 observed in acyl-enzyme complex structures. Together with previous biochemical and NMR studies, these observations indicate that Tyr150 is protonated throughout the reaction coordinate, disfavoring mechanisms that involve a stable tyrosinate as the general base for deacylation. Rather, the hydroxyl of Tyr150 appears to be well positioned to electrostatically stabilize the negative charge buildup in the tetrahedral high-energy intermediate. This structure, in itself, appears consistent with a mechanism involving either Tyr150 acting as a transient catalytic base in conjunction with a neutral Lys67 or the lactam nitrogen as the general base. Whereas mutagenesis studies suggest that Lys67 may be replaced by an arginine, disfavoring the conjugate base mechanism, distinguishing between these two hypotheses may ultimately depend on direct determination of the pK(a) of Lys67 along the reaction coordinate.

PubMed: 16506777
DOI: 10.1021/ja056806m

Experimental method

X-RAY DIFFRACTION (1.07 Å)