NMR structure of holo-acp

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Decrypting the programming of beta-methylation in virginiamycin M biosynthesis.

Collin, S.Cox, R.J.Paris, C.Jacob, C.Chagot, B.Weissman, K.J.Gruez, A.

(2023) Nat Commun 14: 1327-1327

  • DOI: https://doi.org/10.1038/s41467-023-36974-3
  • Primary Citation of Related Structures:  
    8A7Z, 8AHQ, 8AHZ, 8AIG, 8ALL

  • PubMed Abstract: 

    During biosynthesis by multi-modular trans-AT polyketide synthases, polyketide structural space can be expanded by conversion of initially-formed electrophilic β-ketones into β-alkyl groups. These multi-step transformations are catalysed by 3-hydroxy-3-methylgluratryl synthase cassettes of enzymes. While mechanistic aspects of these reactions have been delineated, little information is available concerning how the cassettes select the specific polyketide intermediate(s) to target. Here we use integrative structural biology to identify the basis for substrate choice in module 5 of the virginiamycin M trans-AT polyketide synthase. Additionally, we show in vitro that module 7, at minimum, is a potential additional site for β-methylation. Indeed, analysis by HPLC-MS coupled with isotopic labelling and pathway inactivation identifies a metabolite bearing a second β-methyl at the expected position. Collectively, our results demonstrate that several control mechanisms acting in concert underpin β-branching programming. Furthermore, variations in this control - whether natural or by design - open up avenues for diversifying polyketide structures towards high-value derivatives.

  • Organizational Affiliation

    Université de Lorraine, CNRS, IMoPA, F-54000, Nancy, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hybrid polyketide synthase-non ribosomal peptide synthetase85Streptomyces virginiaeMutation(s): 0 
Gene Names: virA
Find proteins for A4PHN0 (Streptomyces virginiae)
Explore A4PHN0 
Go to UniProtKB:  A4PHN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4PHN0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNS (Subject of Investigation/LOI)
Query on PNS

Download Ideal Coordinates CCD File 
C11 H23 N2 O7 P S
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references