Structure of the lipopeptide antibiotic tsushimycin

Abstract

The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding.

A High‐Resolution Crystal Structure that Reveals Molecular Details of Target Recognition by the Calcium‐Dependent Lipopeptide Antibiotic Laspartomycin C

“…Structural features that are important for dimer formation and Ca 2+ binding are predominantly conserved within the CDA family. Notably, the structure of the unliganded tsushimycin/Ca 2+ complex is also dimeric15 and superimposes closely to our laspartomycin C dimer in complex with Ca 2+ and C 10 ‐P (Supporting Information, Table S7, Figure S17). Whether this indicates that the structures of all CDAs are similar and whether they all form dimers awaits further experimental verification.…”

“…Notably, the sequestration of C 55 ‐P is a mechanism not exploited by any current clinically used antibiotic making it an attractive target for further study. To date, the only structural insights available for the C 55 ‐P binding CDAs are provided by the unliganded structure of tsushimycin 15. To achieve a deeper understanding of the high‐affinity C 55 ‐P binding and specificity, herein we report the crystal structure of laspartomycin C in complex with calcium and geranyl phosphate (C 10 ‐P, a soluble C 55 ‐P analogue) at a resolution of 1.28 Å.…”

The action mechanism of daptomycin

“…The acyl chain and the hydrophobic Trp (1) and Kyn (13) residues were clustered at one end of the hairpin, while polar neutral and ionic residues were situated at the other. Asp (5) Asp (7) B D-Asp (2) Asp (7) Asp (9) mGlu (12) Figure 4: Crystal structure of tsushimycin, 46 and NMR structure of daptomycin. 42 A: In tsushimycin, Ca 2+ is coordinated by Asp (5) together with several backbone carbonyls from the ring.…”

“…Rotondi and Gierasch 39 as well as Bunkoczi et al 46 pointed out that, since Straus et al had used conditions of incipient aggregation, some or all of their measured medium and long range NOEs might have arisen from intermolecular interactions. Realizing that daptomycin aggregation may have affected their results, Straus et al re-examined their Ca 2+ -bound daptomycin structure in detail.…”

“…However, the crystal structure of another cyclic lipopeptide antibiotic, tsushimycin (Figure 1), has been determined at 1.0 Å resolution. 46 The peptide backbone resembles a saddle with a long tail. A Ca 2+ ion is bound in the middle of the saddle by interaction with the side-chains of two Asp groups (Asp (1) and Asp (5) ), four backbone carbonyl O atoms (Dab (2) , Gly (6) , Gly (8) and Val (10) ), and a water molecule (see Figure 4A).…”