9UGQ

Cryo-EM structure of ClassIII Salivaricin modification enzyme SalKC in the presence of SalA

Summary for 9UGQ

• Entry DOI: 10.2210/pdb9ugq/pdb
• EMDB information: 64143
• Descriptor: SalKC, SalA, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, ... (4 entities in total)
• Functional Keywords: lanthibiotic, ripps, lankc, cryoem, antimicrobial peptides, antimicrobial protein
• Biological source: Streptococcus salivarius; More
• Total number of polymer chains: 3
• Total formula weight: 203264.03

Authors

Li, Y.,Luo, M.,Shao, K.,Li, Y. (deposition date: 2025-04-13, release date: 2025-09-03, Last modification date: 2025-10-01)

Primary citation

Li, Y.,Shao, K.,Li, Y.,Gan, B.K.,Luo, M.
Structural Basis of Substrate Recognition and Nucleotide Specificity in the Class III-b LanKC Enzyme SalKC.
Acs Chem.Biol., 20:2255-2265, 2025

PubMed Abstract: Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) with potent antimicrobial functions. Their biosynthesis is carried out by dedicated biosynthetic enzymes, including the recently described Class III-b LanKC enzymes, which represent a newly defined subclass of trifunctional synthetases. Here, we report the high-resolution cryo-EM structure and biochemical characterization of SalKC from , which catalyzes the maturation of the antimicrobial peptide salivaricin. SalKC adopts a conserved dimeric architecture stabilized by a His36 hotspot, mirroring that of the previously characterized PneKC. Cryo-EM structure resolved to sub-3.0 Å revealed the side chains of the bound leader peptide in atomic detail, allowing clear visualization of a conserved recognition motif and offering new structural insight into peptide engagement. Biochemical assays showed that SalKC prefers ATP over GTP, contrasting with the GTP-preferring PneKC. Structural comparison identified a single amino acid switch: Lys303 in SalKC versus His300 in PneKC, as the key determinant of this specificity. Mutation of Lys303 to histidine reverses nucleotide preference, confirming its functional role. Together, these findings revealed conserved principles and specialized adaptations within Class III-b LanKC enzymes and provided a molecular framework for understanding their substrate and cofactor selectivity.

PubMed: 40882187
DOI: 10.1021/acschembio.5c00378

Experimental method

ELECTRON MICROSCOPY (2.96 Å)