8AHZ

Native VirD of Streptomyces virginiae


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase
A, B, C
250Streptomyces virginiaeMutation(s): 0 
Gene Names: virD
UniProt
Find proteins for A4PHM7 (Streptomyces virginiae)
Explore A4PHM7 
Go to UniProtKB:  A4PHM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4PHM7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
S [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
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)
Query on CL

Download Ideal Coordinates CCD File 
FA [auth B],
QA [auth C],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 = 84.31α = 90
b = 84.31β = 90
c = 230.19γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-11-JSV8-003-01
Agence Nationale de la Recherche (ANR)FranceANR-16-CE92-0006-01
Agence Nationale de la Recherche (ANR)FranceANR-20-CE93-0002-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary