6HHZ

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine

Summary for 6HHZ

• Entry DOI: 10.2210/pdb6hhz/pdb
• Related: 6HDZ 6HE1 6HE3 6HHV 6HHW 6HHX 6HHY 6HI0
• Descriptor: Serine--tRNA ligase, 1,2-ETHANEDIOL, 5'-O-(N-(L-seryl)-sulfamoyl)cytidine, ... (7 entities in total)
• Functional Keywords: coil-coil, beta barrel, trna synthetase, inhibitor, complex, ligase
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 49658.72

Authors

Pang, L.,De Graef, S.,Weeks, S.D.,Strelkov, S.V. (deposition date: 2018-08-29, release date: 2019-12-18, Last modification date: 2024-01-17)

Primary citation

Pang, L.,Nautiyal, M.,De Graef, S.,Gadakh, B.,Zorzini, V.,Economou, A.,Strelkov, S.V.,Van Aerschot, A.,Weeks, S.D.
Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases.
Acs Chem.Biol., 15:407-415, 2020

PubMed Abstract: The pyrimidine-containing Trojan horse antibiotics albomycin and a recently discovered cytidine-containing microcin C analog target the class II seryl- and aspartyl-tRNA synthetases (serRS and aspRS), respectively. The active components of these compounds are competitive inhibitors that mimic the aminoacyl-adenylate intermediate. How they effectively substitute for the interactions mediated by the canonical purine group is unknown. Employing nonhydrolyzable aminoacyl-sulfamoyl nucleosides substituting the base with cytosine, uracil, and N3-methyluracil the structure-activity relationship of the natural compounds was evaluated. using serRS and aspRS, the best compounds demonstrated IC values in the low nanomolar range, with a clear preference for cytosine or N3-methyluracil over uracil. X-ray crystallographic structures of serRS and aspRS in complex with the compounds showed the contribution of structured waters and residues in the conserved motif-2 loop in defining base preference. Utilizing the N3-methyluracil bound serRS structure, MD simulations of the fully modified albomycin base were performed to identify the interacting network that drives stable association. This analysis pointed to key interactions with a methionine in the motif-2 loop. Interestingly, this residue is mutated to a glycine in a second serRS (serRS2) found in albomycin-producing actinobacteria possessing self-immunity to this antibiotic. A comparative study demonstrated that serRS2 is poorly inhibited by the pyrimidine-containing intermediate analogs, and an equivalent mutation in serRS significantly decreased the affinity of the cytosine congener. These findings highlight the crucial role of dynamics and solvation of the motif-2 loop in modulating the binding of the natural antibiotics.

PubMed: 31869198
DOI: 10.1021/acschembio.9b00887

Experimental method

X-RAY DIFFRACTION (2.15 Å)