8VPO

X-Ray Crystal Structure of TigE from Paramaledivibacter caminithermalis

Summary for 8VPO

• Entry DOI: 10.2210/pdb8vpo/pdb
• Descriptor: Radical SAM core domain-containing protein, IRON/SULFUR CLUSTER, GLYCEROL, ... (4 entities in total)
• Functional Keywords: radical sam, fe-s cluster, cyclopropylglycine, ripp, oxidoreductase
• Biological source: Paramaledivibacter caminithermalis
• Total number of polymer chains: 1
• Total formula weight: 55736.37

Authors

Grove, T.L.,Lachowicz, J.C.,Zizola, C. (deposition date: 2024-01-16, release date: 2024-02-07, Last modification date: 2024-02-28)

Primary citation

Lien, Y.,Lachowicz, J.C.,Mendauletova, A.,Zizola, C.,Ngendahimana, T.,Kostenko, A.,Eaton, S.S.,Latham, J.A.,Grove, T.L.
Structural, Biochemical, and Bioinformatic Basis for Identifying Radical SAM Cyclopropyl Synthases.
Acs Chem.Biol., 19:370-379, 2024

PubMed Abstract: The importance of radical S-adenosyl-l-methionine (RS) enzymes in the maturation of ribosomally synthesized and post-translationally modified peptides (RiPPs) continues to expand, specifically for the RS-SPASM subfamily. We recently discovered an RS-SPASM enzyme that installs a carbon-carbon bond between the geminal methyls of valine residues, resulting in the formation of cyclopropylglycine (CPG). Here, we sought to define the family of cyclopropyl (CP) synthases because of the importance of cyclopropane scaffolds in pharmaceutical development. Using RadicalSAM.org, we bioinformatically expanded the family of CP synthases and assigned unique peptide sequences to each subclade. We identified a unique RiPP biosynthetic pathway that encodes a precursor peptide, TigB, with a repeating TIGSVS motif. Using LCMS and NMR techniques, we show that the RS enzyme associated with the pathway, TigE, catalyzes the formation of a methyl-CPG from the conserved isoleucine residing in the repeating motif of TigB. Furthermore, we obtained a crystal structure of TigE, which reveals an unusual tyrosyl ligation to the auxiliary I [4Fe-4S] cluster, provided by a glycine-tyrosine-tryptophan motif unique to all CP synthases. Further, we show that this unique tyrosyl ligation is absolutely required for TigE activity. Together, our results provide insight into how CP synthases perform this unique reaction.

PubMed: 38295270
DOI: 10.1021/acschembio.3c00583

Experimental method

X-RAY DIFFRACTION (1.66 Å)