The Oxyanion Hole in Serine β-Lactamase Catalysis: Interactions of Thiono Substrates with the Active Site

Curley, Kieran; Pratt, Robertson

doi:10.1006/bioo.2000.1184

Cited by 12 publications

(9 citation statements)

References 68 publications

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“…The carbonyl oxygen atom (O7, Fig. 3b ) of the hydrolyzed β-lactam ring of doripenem sits in a small pocket generally referred to as the oxyanion hole 33 , 34 , between the N-terminus of helix α3 and the side of strand β8. In BPU-1 the O7 atom accepts hydrogen bonds from the amide nitrogen atoms of Ser101 and Ser242 ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Class D β-lactamases do exist in Gram-positive bacteria

et al. 2015

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Production of β-lactamases of the four molecular classes (A, B, C, and D) is the major mechanism of bacterial resistance to β-lactams, the largest class of antibiotics that have saved countless lives since their inception 70 years ago. Although several hundred efficient class D enzymes have been identified in Gram-negative pathogens over the last four decades, they have not been reported in Gram-positive bacteria. Here we demonstrate that efficient class D β-lactamases capable of hydrolyzing a wide array of β-lactam substrates are widely disseminated in various species of environmental Gram-positive organisms. Class D enzymes of Gram-positive bacteria have a distinct structural architecture and employ a unique substrate binding mode quite different from that of all currently known class A, C, and D β-lactamases. They constitute a novel reservoir of antibiotic resistance enzymes.

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Section: Resultsmentioning

confidence: 99%

Class D β-lactamases do exist in Gram-positive bacteria

et al. 2015

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“…This strand contributes two residues Atomic Resolution of CTX-M b-Lactamases essential to catalytic activity, Lys234 and the main chain of Ser237, which forms part of the enzyme's "oxyanion" hole, 38,39 and several substraterecognition residues. In the CTX-M ESBLs, unlike those of TEM and SHV, increased activity against the bulky third-generation cephalosporins, especially ceftazidime, appears to come not from gross enlargement of the active site, but from increased flexibility of this strand, and possibly other regions.…”

Section: Activity and Stability Tradeoffmentioning

confidence: 99%

Atomic Resolution Structures of CTX-M β-Lactamases: Extended Spectrum Activities from Increased Mobility and Decreased Stability

Chen

Delmas

Sirot

et al. 2005

Journal of Molecular Biology

135

190

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“…A water molecule (Wat74) is hydrogen bonded to the Oγ atom of both Ser102 conformers and to the main chain nitrogen atoms of Ser102 and Thr254, which together form the oxyanion hole, a conserved feature of the serine β-lactamase active site. 38 A second well-ordered water molecule (Wat76) bridges between the Ser102 con-former A side chain and the carboxylated lysine (hereinafter designated Lys105 CO2 ). In the initial 2F o -F c and F o -F c electron density maps, residual density attached to the end of the Lys105 side chain suggested the presence of the carboxylate moiety (Figures 2 and 3A), which refined to a group occupancy of 0.80.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…The active site serine (Ser102) is initially present in two conformations, one (conformer A ) ideally poised to form the acyl bond to a bound substrate with an occupancy of 0.55, and the other (conformer B ) directed toward strand β8. A water molecule (Wat74) is hydrogen bonded to the Oγ atom of both Ser102 conformers and to the main chain nitrogen atoms of Ser102 and Thr254, which together form the oxyanion hole, a conserved feature of the serine β-lactamase active site . A second well-ordered water molecule (Wat76) bridges between the Ser102 conformer A side chain and the carboxylated lysine (hereinafter designated Lys105 CO2 ).…”

Section: Resultsmentioning

confidence: 99%

In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases

et al. 2021

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Class D β-lactamases have risen to notoriety due to their wide spread in bacterial pathogens, propensity to inactivate clinically important β-lactam antibiotics, and ability to withstand inhibition by the majority of classical β-lactamase inhibitors. Understanding the catalytic mechanism of these enzymes is thus vitally important for the development of novel antibiotics and inhibitors active against infections caused by antibiotic-resistant bacteria. Here we report an in crystallo time-resolved study of the interaction of the class D β-lactamase CDD-1 from Clostridioides difficile with the diazobicyclooctane inhibitor, avibactam. We show that the catalytic carboxylated lysine, a residue that is essential for both acylation and deacylation of β-lactams, is sequestered within an internal sealed pocket of the enzyme. Time-resolved snapshots generated in this study allowed us to observe decarboxylation of the lysine and movement of CO2 and water molecules through a transient channel formed between the lysine pocket and the substrate binding site facilitated by rotation of the side chain of a conserved leucine residue. These studies provide novel insights on avibactam binding to CDD-1 and into the catalytic mechanism of class D β-lactamases in general.

show abstract

The Oxyanion Hole in Serine β-Lactamase Catalysis: Interactions of Thiono Substrates with the Active Site

Cited by 12 publications

References 68 publications

Class D β-lactamases do exist in Gram-positive bacteria

Class D β-lactamases do exist in Gram-positive bacteria

Atomic Resolution Structures of CTX-M β-Lactamases: Extended Spectrum Activities from Increased Mobility and Decreased Stability

In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases

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