8C0U

1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with their natural substrates and products

Summary for 8C0U

• Entry DOI: 10.2210/pdb8c0u/pdb
• Related: 8BRE
• Descriptor: Anhydro-N-acetylmuramic acid kinase, ADENOSINE-5'-DIPHOSPHATE, 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID, ... (5 entities in total)
• Functional Keywords: anhydro-sugar kinase phosphotransferase atp binding, transferase
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 2
• Total formula weight: 80450.56

Authors

Jimenez-Faraco, E.,Hermoso, J.A. (deposition date: 2022-12-19, release date: 2023-09-20, Last modification date: 2023-10-25)

Primary citation

El-Araby, A.M.,Jimenez-Faraco, E.,Feltzer, R.,Martin-Garcia, J.M.,Karri, B.R.,Ramachandran, B.,Kim, C.,Fisher, J.F.,Hermoso, J.A.,Mobashery, S.
Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa.
J.Biol.Chem., 299:105198-105198, 2023

PubMed Abstract: The bacterial cell envelope is the structure with which the bacterium engages with, and is protected from, its environment. Within this envelop is a conserved peptidoglycan polymer which confers shape and strength to the cell envelop. The enzymatic processes that build, remodel, and recycle the chemical components of this cross-linked polymer are preeminent targets of antibiotics and exploratory targets for emerging antibiotic structures. We report a comprehensive kinetic and structural analysis for one such enzyme, the Pseudomonas aeruginosa anhydro-N-acetylmuramic acid (anhNAM) kinase (AnmK). AnmK is an enzyme in the peptidoglycan-recycling pathway of this pathogen. It catalyzes the pairing of hydrolytic ring opening of anhNAM with concomitant ATP-dependent phosphoryl transfer. AnmK follows a random-sequential kinetic mechanism with respect to its anhNAM and ATP substrates. Crystallographic analyses of four distinct structures (apo AnmK, AnmK:AMPPNP, AnmK:AMPPNP:anhNAM, and AnmK:ATP:anhNAM) demonstrate that both substrates enter the active site independently in an ungated conformation of the substrate subsites, with protein loops acting as gates for anhNAM binding. Catalysis occurs within a closed conformational state for the enzyme. We observe this state crystallographically using ATP-mimetic molecules. A remarkable X-ray structure for dimeric AnmK sheds light on the precatalytic and postcatalytic ternary complexes. Computational simulations in conjunction with the high-resolution X-ray structures reveal the full catalytic cycle. We further report that a P. aeruginosa strain with disrupted anmK gene is more susceptible to the β-lactam imipenem compared to the WT strain. These observations position AnmK for understanding the nexus among peptidoglycan recycling, susceptibility to antibiotics, and bacterial virulence.

PubMed: 37660917
DOI: 10.1016/j.jbc.2023.105198

Experimental method

X-RAY DIFFRACTION (2.112 Å)