9GN5 | pdb_00009gn5

EpxF in complex with FAD from Goodfellowiella coeruleoviolacea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Studies of alpha ', beta '-Epoxyketone Synthesis by Small-Molecule Flavins and Flavoenzymes.

Walter, A.Kuttenlochner, W.Eisenreich, W.Yao, C.Groll, M.Storch, G.

(2025) Angew Chem Int Ed Engl : e202512568-e202512568

  • DOI: https://doi.org/10.1002/anie.202512568
  • Primary Citation of Related Structures:  
    9GN5

  • PubMed Abstract: 

    Epoxomicin is a highly potent natural proteasome inhibitor and the structural scaffold for the anticancer drug carfilzomib. The biosynthesis of its α',β'-epoxyketone warhead involves the flavoenzyme EpxF, but a molecular understanding of the key catalytic reaction cascade remained elusive. Here, we disclose detailed mechanistic insights by characterizing all intermediates in the sequential steps of decarboxylation, desaturation, and epoxidation with synthetic flavins and the flavin-dependent oxidoreductase EpxF. A high-resolution crystal structure of EpxF revealed the architecture of the active site and enabled the identification of key catalytic residues. Exploratory docking based on this structure served as a qualitative tool to guide mutagenesis and rationalize substrate recognition. NMR studies with a 13 C-labeled epoxomicin precursor and structure-based EpxF variants further supported the proposed mechanism. Our integrated approach revealed similarities between synthetic and natural flavin catalysts and offers avenues for developing sustainable biomimetic reactions.


  • Organizational Affiliation
    • Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EpxF564Goodfellowiella coeruleoviolaceaMutation(s): 0 
Gene Names: epxF
UniProt
Find proteins for V5RNC8 (Goodfellowiella coeruleoviolacea)
Explore V5RNC8 
Go to UniProtKB:  V5RNC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5RNC8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.24α = 90
b = 147.95β = 90
c = 67.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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)Germany325871075 (SFB 1309)

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references