9EHY

X-ray crystal structure of ADC-33 beta-lactamase in complex with ceftazidime in acyl and product forms

This is a non-PDB format compatible entry.

Summary for 9EHY

• Entry DOI: 10.2210/pdb9ehy/pdb
• Descriptor: Beta-lactamase, (2R)-2-[(R)-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}(carboxy)methyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid, ACYLATED CEFTAZIDIME, ... (4 entities in total)
• Functional Keywords: lactamase, complex, cephalosporin, ceftazidime, hydrolase
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 2
• Total formula weight: 83069.58

Authors

Powers, R.A.,Wallar, B.J.,Jarvis, H.R.,Ziegler, Z.X.,June, C.M. (deposition date: 2024-11-25, release date: 2025-05-14, Last modification date: 2025-05-28)

Primary citation

Powers, R.A.,Wallar, B.J.,Jarvis, H.R.,Ziegler, Z.X.,June, C.M.,Bethel, C.R.,Hujer, A.M.,Taracila, M.A.,Rudin, S.D.,Hujer, K.M.,Prati, F.,Caselli, E.,Bonomo, R.A.
Resistance to oxyimino-cephalosporins conferred by an alternative mechanism of hydrolysis by the Acinetobacter -derived cephalosporinase-33 (ADC-33), a class C beta-lactamase present in carbapenem-resistant Acinetobacter baumannii (CR Ab ).
Mbio, :e0028725-e0028725, 2025

PubMed Abstract: Antimicrobial resistance in is partly mediated by chromosomal class C β-lactamases, the -derived cephalosporinases (ADCs). Recently, a growing number of emerging variants were described, expanding this threat. Consistent with other β-lactamases, one of the main areas of variance exists in the Ω-loop region near the site of cephalosporin binding. Interestingly, a common alanine duplication (Adup) is found in this region. Herein, we studied specific Adup variants expressed in a uniform genetic background that demonstrated high-level resistance to multiple oxyimino-cephalosporins. For ceftolozane and ceftazidime, the Adup ADCs significantly increased levels of resistance (minimum inhibitory concentration [MIC] ≥ 512 µg/mL and MIC ≥ 1,024 µg/mL, respectively). These observations were consistent with the increased / for ceftazidime. For cefiderocol, three Adup variants exhibited increased MICs and increased / for this compound. Timed electrospray ionization mass spectrometry demonstrated stable cephalosporin:ADC adducts with ADC-30 (non-Adup), but not with ADC-33 (Adup), consistent with turnover. The X-ray crystal structure of Adup variant ADC-33 in complex with ceftazidime was determined (1.57 Å resolution) and suggests that increased turnover is facilitated by conformational changes (shift in Tyr221 and orientation of the oxyimino portion of the R1 side chain) and repositioning of water in the active site. These changes appear to favor substrate-assisted catalysis as an alternative mechanism to base-assisted catalysis. These studies also provide unprecedented insight into the mechanism underlying oxyimino-cephalosporin hydrolysis by expanded-spectrum ADC β-lactamases and possibly other class C β-lactamases, which is of critical importance to future drug design.IMPORTANCEThe characterization of emerging -derived cephalosporinase (ADC) variants is necessary to understand the increasing resistance to β-lactam antibiotics in spp. In this study, cefiderocol retains effectiveness against ADC variants with and without an Ω-loop alanine duplication (Adup). However, the presence of the Adup appears to introduce loop flexibility and structural alterations resulting in increased resistance and steady-state turnover of larger cephalosporins. Further characterization provides unprecedented insight into the mechanism of cephalosporin hydrolysis by ADC β-lactamases and supports a concomitant increase in ADC structural flexibility and cephalosporin affinity that leads to more efficient hydrolysis. In addition, the crystal structure of ADC-33 in complex with ceftazidime is consistent with a substrate-assisted catalysis mechanism. The structural differences in the ADC-33 active site leading to ceftazidime catalysis provide a better understanding of β-lactamase Adup variants and open important opportunities for future drug design and development.

PubMed: 40377322
DOI: 10.1128/mbio.00287-25

Experimental method

X-RAY DIFFRACTION (1.57 Å)