43CP | pdb_000043cp

Aphotorhaptin A, N-acetylated monocyclic daropeptide from Photorhabdus asymbiotica


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

An N-acetylated daropeptide modulates nematode development.

Ma, S.Li, R.Gao, X.Gemmell, E.Guo, S.Chen, H.Huang, X.Capper, M.Liu, Z.Deng, Z.Ding, W.Kohnke, J.Wang, X.Zhang, Q.

(2026) Proc Natl Acad Sci U S A 123: e2617449123-e2617449123

  • DOI: https://doi.org/10.1073/pnas.2617449123
  • Primary Citation Related Structures: 
    43CP

  • PubMed Abstract: 

    The symbiotic bacterium Photorhabdus is a rich source of bioactive secondary metabolites that mediate tripartite interactions with nematodes and insect hosts. However, natural products of ribosomal origin remain largely underexplored within this ecological niche. Here, we report the identification of aphotorhaptin A, a darobactin-like peptide (daropeptide) natural product from Photorhabdus asymbiotica , which structurally features an ether crosslink and an N-terminal acetyl unit. Biosynthetic investigation uncovers aphotorhaptin A is matured via an unexpected leader cleavage step, and the subsequent N-terminal acetylation confers metabolic stability that maintains the hexapeptide scaffold integrity. Biochemical and structural studies demonstrate the acetyltransferase PasC exhibits remarkable substrate promiscuity, facilitated by an expansive active-site cavity that accommodates diverse acyl-CoA donors and peptide substrates. Unlike the antimicrobial darobactin, aphotorhaptin A appears to lack antibacterial activity but modulates nematode development, and this activity requires the ether crosslink and the N-terminal acetyl group in the hexapeptide scaffold. These findings expand the chemical and biosynthetic space of ribosomal peptide family and establish its link with nematode development and reproduction.


  • Organizational Affiliation
    • National Engineering Research Center for Carbohydrate Synthesis, College of Chemistry and Materials, Jiangxi Normal University, Nanchang 330022, China.

Macromolecule Content 

  • Total Structure Weight: 0.93 kDa 
  • Atom Count: 68 
  • Modeled Residue Count: 7 
  • Deposited Residue Count: 7 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACE-GLN-UN8-THR-PHE-ARG-PHE7Photorhabdus asymbioticaMutation(s): 0 
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0AF
Query on 0AF
A
L-PEPTIDE LINKINGC11 H12 N2 O3TRP

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China223B2701
National Science Foundation (NSF, China)China32070050
National Science Foundation (NSF, China)China32270070
National Science Foundation (NSF, China)China21921003
National Science Foundation (NSF, China)ChinaU22A20451

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-05
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Database references