7PCN

BurG (holo) in complex with gonyenediol (14), trigonic acid (6) and DMS: Biosynthesis of cyclopropanol rings in bacterial toxins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.

Trottmann, F.Ishida, K.Ishida-Ito, M.Kries, H.Groll, M.Hertweck, C.

(2022) Nat Chem 14: 884-890

  • DOI: https://doi.org/10.1038/s41557-022-01005-z
  • Primary Citation of Related Structures:  
    7PCC, 7PCE, 7PCG, 7PCI, 7PCL, 7PCM, 7PCN, 7PCO, 7PCT

  • PubMed Abstract: 

    Bacteria of the Burkholderia pseudomallei (BP) group pose a global health threat, causing the infectious diseases melioidosis, a common cause of pneumonia and sepsis, and glanders, a contagious zoonosis. A trait of BP bacteria is a conserved gene cluster coding for the biosynthesis of polyketides (malleicyprols) with a reactive cyclopropanol unit that is critical for virulence. Enzymes building this warhead represent ideal targets for antivirulence strategies but the biochemical basis of cyclopropanol formation is unknown. Here we describe the formation of the malleicyprol warhead. We show that BurG, an unusual NAD + -dependent member of the ketol-acid reductoisomerase family, constructs the strained cyclopropanol ring. Biochemical assays and a suite of eight crystal structures of native and mutated BurG with bound analogues and inhibitors provide snapshots of each step of the complex reaction mechanism, involving a concealed oxidoreduction and a C-S bond cleavage. Our findings illustrate a remarkable case of neofunctionalisation, where a biocatalyst from central metabolism has been evolutionarily repurposed for warhead production in pathogens.


  • Organizational Affiliation

    Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketol-acid reductoisomerase
A, B
358Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: ilvC-2BTH_II2094
EC: 1.1.1.86
UniProt
Find proteins for Q2T3G7 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264))
Explore Q2T3G7 
Go to UniProtKB:  Q2T3G7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2T3G7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
7BI (Subject of Investigation/LOI)
Query on 7BI

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
dimethyl-[(Z)-3,4,5-tris(oxidanyl)-5-oxidanylidene-pent-3-enyl]sulfanium
C7 H13 O4 S
OURROQZHBYSLDP-WAYWQWQTSA-O
78I (Subject of Investigation/LOI)
Query on 78I

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
(2R)-2-oxidanyl-2-(1-oxidanylcyclopropyl)ethanoic acid
C5 H8 O4
XIFMBZFYSIRQIK-VKHMYHEASA-N
MSM (Subject of Investigation/LOI)
Query on MSM

Download Ideal Coordinates CCD File 
F [auth A],
N [auth B]
(METHYLSULFANYL)METHANE
C2 H6 S
QMMFVYPAHWMCMS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
L [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.88α = 90
b = 76.13β = 105.14
c = 79.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 1309 - 325871075

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description