High adaptability of the omega loop underlies the substrate-spectrum-extension evolution of a class A β-lactamase, PenL.
The omega loop in β-lactamases plays a pivotal role in substrate recognition and catalysis, and some mutations in this loop affect the adaptability of the enzymes to new antibiotics. Various mutations, including substitutions, deletions, and intragenic duplications resulting in tandem repeats (TRs), have been associated with β-lactamase substrate spectrum extension. TRs are unique among the mutations as they cause severe structural perturbations in the enzymes. We explored the process by which TRs are accommodated in order to test the adaptability of the omega loop. Structures of the mutant enzymes showed that the extra amino acid residues in the omega loop were freed outward from the enzyme, thereby maintaining the overall enzyme integrity. This structural adjustment was accompanied by disruptions of the internal α-helix and hydrogen bonds that originally maintained the conformation of the omega loop and the active site. Consequently, the mutant enzymes had a relaxed binding cavity, allowing for access of new substrates, which regrouped upon substrate binding in an induced-fit manner for subsequent hydrolytic reactions. Together, the data demonstrate that the design of the binding cavity, including the omega loop with its enormous adaptive capacity, is the foundation of the continuous evolution of β-lactamases against new drugs.
Department of Biomedical Sciences, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-705, Korea.
Hyojeong
H
Yi
Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, Korea.
Jin Myung
JM
Choi
Department of Biomedical Sciences, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-705, Korea.
Junghyun
J
Hwang
Department of Life Sciences, University of Modena, Modena 41125, Italy.
Fabio
F
Prati
Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, Korea.
Thinh-Phat
TP
Cao
Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, Korea.
Sung Haeng
SH
Lee
Department of Biomedical Sciences, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-705, Korea.
Heenam Stanley
HS
Kim
D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology; D002442:Ceftazidime / Q000494:pharmacology; D008826:Microbial Sensitivity Tests; D015394:Molecular Structure; D009154:Mutation; D013379:Substrate Specificity; D020080:Tandem Repeat Sequences; D001618:beta-Lactamases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
D000900:Anti-Bacterial Agents; D002442:Ceftazidime; D001618:beta-Lactamases