8JTP

Crystal structure of apo Enoyl-Acyl Carrier Protein Reductase (FabI) from Klebsiella pneumoniae

Summary for 8JTP

• Entry DOI: 10.2210/pdb8jtp/pdb
• Descriptor: Enoyl-[acyl-carrier-protein] reductase [NADH], HEXAETHYLENE GLYCOL (3 entities in total)
• Functional Keywords: klebsiella pneumoniae, enoyl-acyl carrier protein reductase, fabi, fatty acid biosynthesis, enr, oxidoreductase
• Biological source: Klebsiella pneumoniae subsp. pneumoniae
• Total number of polymer chains: 4
• Total formula weight: 113171.58

Authors

Biswas, S.,Kushwaha, G.S.,Suar, M. (deposition date: 2023-06-22, release date: 2023-12-06, Last modification date: 2024-04-03)

Primary citation

Biswas, S.,Patra, A.,Paul, P.,Misra, N.,Kushwaha, G.S.,Suar, M.
Structural and Biochemical Studies on Klebsiella Pneumoniae Enoyl-ACP Reductase (FabI) Suggest Flexible Substrate Binding Site.
Protein J., 43:84-95, 2024

PubMed Abstract: Klebsiella pneumoniae, a bacterial pathogen infamous for antibiotic resistance, is included in the priority list of pathogens by various public health organizations due to its extraordinary ability to develop multidrug resistance. Bacterial fatty acid biosynthesis pathway-II (FAS-II) has been considered a therapeutic drug target for antibacterial drug discovery. Inhibition of FAS-II enzyme, enoyl-acyl carrier protein reductase, FabI, not only inhibits bacterial infections but also reverses antibiotic resistance. Here, we characterized Klebsiella pneumoniae FabI (KpFabI) using complementary experimental approaches including, biochemical, x-ray crystallography, and molecular dynamics simulation studies. Biophysical studies shows that KpFabI organizes as a tetramer molecular assembly in solution as well as in the crystal structure. Enzyme kinetics studies reveal a distinct catalytic property towards crotonyl CoA and reducing cofactor NADH. Michaelis-Menten constant (K) values of substrates show that KpFabI has higher preference towards NADH as compared to crotonyl CoA. The crystal structure of tetrameric apo KpFabI folds into a classic Rossman fold in which β-strands are sandwiched between α-helices. A highly flexible substrate binding region is located toward the interior of the tetrameric assembly. Thermal stability assay on KpFabI with its substrate shows that the flexibility is primarily stabilized by cofactor NADH. Moreover, the molecular dynamics further supports that KpFabI has highly flexible regions at the substrate binding site. Together, these findings provide evidence for highly dynamic substrate binding sites in KpFabI, therefore, this information will be vital for specific inhibitors discovery targeting Klebsiella pneumoniae.

PubMed: 38127182
DOI: 10.1007/s10930-023-10176-8

Experimental method

X-RAY DIFFRACTION (2.9 Å)