1W3M

Crystal structure of tsushimycin

Summary for 1W3M

• Entry DOI: 10.2210/pdb1w3m/pdb
• Related PRD ID: PRD_000487
• Descriptor: TSUSHIMYCIN, Delta-3isotetradecenoic acid, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: amphomycin, daptomycin, lipopetide, antibiotic, antibacterial
• Biological source: ACTINOPLANES FRIULIENSIS
• Total number of polymer chains: 12
• Total formula weight: 18225.35

Authors

Bunkoczi, G.,Vertesy, L.,Sheldrick, G.M. (deposition date: 2004-07-16, release date: 2005-07-27, Last modification date: 2025-04-09)

Primary citation

Bunkoczi, G.,Vertesy, L.,Sheldrick, G.M.
Structure of the lipopeptide antibiotic tsushimycin.
Acta Crystallogr. D Biol. Crystallogr., 61:1160-1164, 2005

PubMed 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.

PubMed: 16041082
DOI: 10.1107/S0907444905017270

Experimental method

X-RAY DIFFRACTION (1 Å)