Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 81.48 kDa 
• Atom Count: 5,851 
• Modelled Residue Count: 684 
• Deposited Residue Count: 750 
• Unique protein chains: 1

 8AHZ

Native VirD of Streptomyces virginiae

• PDB DOI: 10.2210/pdb8AHZ/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces virginiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-07-25 Released: 2023-03-15 
• Deposition Author(s): Collin, S., Gruez, A.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.180 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Literature

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

• PubMed: 36899003 
• DOI: 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.

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Organizational Affiliation: 

Université de Lorraine, CNRS, IMoPA, F-54000, Nancy, France. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase	A, B, C	250	Streptomyces virginiae	Mutation(s): 0  Gene Names: virD
UniProt
Find proteins for A4PHM7 (Streptomyces virginiae) Explore A4PHM7  Go to UniProtKB:  A4PHM7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	S [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	FA [auth B], QA [auth C], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.180 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.31	α = 90
b = 84.31	β = 90
c = 230.19	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Collin, S., Gruez, A.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-11-JSV8-003-01
Agence Nationale de la Recherche (ANR)	France	ANR-16-CE92-0006-01
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE93-0002-01

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2023-03-22
  Changes: Database references