9GM0 | pdb_00009gm0

KvPepI F420-dependent oxidoreductase, F420 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.181 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Tandem ketone reduction in pepstatin biosynthesis reveals an F 420 H 2 -dependent statine pathway.

Mo, J.Sikandar, A.Zhao, H.Bashiri, G.Huo, L.Empting, M.Muller, R.Fu, C.

(2025) Nat Commun 16: 4531-4531

  • DOI: https://doi.org/10.1038/s41467-025-59785-0
  • Primary Citation of Related Structures:  
    9G64, 9GKH, 9GM0, 9GNC, 9GND

  • PubMed Abstract: 

    Pepstatins are potent inhibitors of aspartic proteases, featuring two statine residues crucial for target binding. However, the biosynthesis of pepstatins, especially their statine substructure, remains elusive. Here, we discover and characterize an unconventional gene cluster responsible for pepstatin biosynthesis, comprising discrete nonribosomal peptide synthetase and polyketide synthase genes, highlighting its trans-acting and iterative nature. Central to this pathway is PepI, an F 420 H 2 -dependent oxidoreductase. The biochemical characterization of PepI reveals its role in the tandem reduction of β-keto pepstatin intermediates. PepI first catalyzes the formation of the central statine, then produces the C-terminal statine moiety. The post-assembly-line formation of statine by PepI contrasts with the previously hypothesized biosynthesis involving polyketide synthase ketoreductase domains. Structural studies, site-directed mutagenesis, and deuterium-labeled enzyme assays probe the mechanism of F 420 H 2 -dependent oxidoreductases and identify critical residues. Our findings uncover a unique statine biosynthetic pathway employing the only known iterative F 420 H 2 -dependent oxidoreductase to date.


  • Organizational Affiliation

    Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative F420-dependent oxidoreductase
A, B
308StreptomycesMutation(s): 0 
Gene Names: FHX73_11672
UniProt
Find proteins for A0A561UC02 (Kitasatospora viridis)
Explore A0A561UC02 
Go to UniProtKB:  A0A561UC02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A561UC02
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F42 (Subject of Investigation/LOI)
Query on F42

Download Ideal Coordinates CCD File 
C [auth A]COENZYME F420
C29 H36 N5 O18 P
GEHSZWRGPHDXJO-NALJQGANSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.181 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.353α = 90
b = 94.271β = 90
c = 111.024γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release