8T2C

Crystal structure of O-acetyl-L-serine sulfhydrylase A (CysK) from Staphylococcus aureus NCTC 8325 complexed with a CymR pentapeptide

Summary for 8T2C

• Entry DOI: 10.2210/pdb8t2c/pdb
• Related: 8SRT 8SRU 8SRV 8SRW
• Descriptor: Cysteine synthase, TYR-MET-PHE-TYR-ILE (3 entities in total)
• Functional Keywords: cysk, cysteine synthesis, cymr, protein binding
• Biological source: Staphylococcus aureus subsp. aureus NCTC 8325; More
• Total number of polymer chains: 4
• Total formula weight: 66936.13

Authors

Pederick, J.L.,Bruning, J.B.,Vandborg, B. (deposition date: 2023-06-05, release date: 2024-12-18, Last modification date: 2025-05-28)

Primary citation

Pederick, J.L.,Vandborg, B.C.,George, A.,Bovermann, H.,Boyd, J.M.,Freundlich, J.S.,Bruning, J.B.
Identification of Cysteine Metabolism Regulator (CymR)-Derived Pentapeptides as Nanomolar Inhibitors of Staphylococcus aureus O -Acetyl-l-serine Sulfhydrylase (CysK).
Acs Infect Dis., 11:238-248, 2025

PubMed Abstract: The pathway of bacterial cysteine biosynthesis is gaining traction for the development of antibiotic adjuvants. Bacterial cysteine biosynthesis is generally facilitated by two enzymes possessing -acetyl-l-serine sulfhydrylases (OASS), CysK and CysM. In , there exists a single OASS homologue, CysK. Knockout of CysK was found to increase sensitivity to oxidative stress, making it a relevant target for inhibitor development. CysK also forms two functional complexes via interaction with the preceding enzyme in the pathway serine acetyltransferase (CysE) or the transcriptional regulator of cysteine metabolism (CymR). These interactions occur through insertion of a C-terminal peptide of CysE or CymR into the active site of CysK, inhibiting OASS activity, and therefore represent an excellent starting point for developing CysK inhibitors. Here, we detail the characterization of CysE and CymR-derived C-terminal peptides as inhibitors of CysK. Using a combination of X-ray crystallography, surface plasmon resonance, and enzyme inhibition assays, it was determined that the CymR-derived decapeptide forms extensive interactions with CysK and acts as a potent inhibitor ( = 25 nM; IC = 180 nM), making it a promising lead for the development of CysK inhibitors. To understand the determinants of this high-affinity interaction, the structure-activity relationships of 16 rationally designed peptides were also investigated. This identified that the C-terminal pentapeptide of CymR facilitates the high-affinity interaction with CysK and that subtle structural modification of the pentapeptide is possible without impacting potency. Ultimately, this work identified CymR pentapeptides as a promising scaffold for the development of antibiotic adjuvants targeting CysK.

PubMed: 39705018
DOI: 10.1021/acsinfecdis.4c00832

Experimental method

X-RAY DIFFRACTION (1.8 Å)