Closthioamide (CTA) is a potent antibiotic with a unique polythioamide scaffold produced by Ruminiclostridium cellulolyticum. Unlike classical non-ribosomal peptide synthetases (NRPSs), which use modular adenylation and condensation domains, CTA biosynthesis proceeds through non-canonical standalone enzymes. Central to this process is the papain-like ligase CtaG, which catalyzes amide bond formation between two distinct peptidyl carrier proteins (PCPs): CtaH, presenting para-hydroxybenzoic acid (PHBA), and CtaE, carrying a tri-β-alanine ((βAla)₃) chain. Using biochemical assays, chemical probes, crystallography, and mutational analysis, we show that CtaG operates via a ping-pong mechanism involving an enzyme-bound intermediate. A single substrate tunnel mediates directional transfer, enabling distal chain elongation that mirrors solid-phase peptide synthesis. Structure-based genome mining revealed homologous enzymes in the biosynthetic pathways of petrobactin, butirosin, and methylolanthanin. Together, our findings uncover a previously overlooked class of thiotemplated ligases and provide a mechanistic blueprint for engineering ribosome-independent peptide assembly lines.