6OGO

Crystal structure of NDM-9 metallo-beta-lactamase

Summary for 6OGO

• Entry DOI: 10.2210/pdb6ogo/pdb
• Descriptor: SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9, ZINC ION, CHLORIDE ION, ... (9 entities in total)
• Functional Keywords: metallo-beta-lactamase, ndm, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 79220.55

Authors

Raczynska, J.E.,Imiolczyk, B.,Jaskolski, M. (deposition date: 2019-04-03, release date: 2020-04-15, Last modification date: 2023-10-11)

Primary citation

Raczynska, J.E.,Imiolczyk, B.,Komorowska, M.,Sliwiak, J.,Czyrko-Horczak, J.,Brzezinski, K.,Jaskolski, M.
Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates.
Int.J.Biol.Macromol., 158:104-115, 2020

PubMed Abstract: Two accessory loop regions that are present in numerous variants of New Delhi metallo-β-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Ω loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Ω loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Ω loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Ω loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the β-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins.

PubMed: 32353499
DOI: 10.1016/j.ijbiomac.2020.04.219

Experimental method

X-RAY DIFFRACTION (1.43 Å)