9IWV | pdb_00009iwv

Crystal structure of Lsd18 after incubation with the substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.230 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Mechanistic and molecular insights into iterative triepoxidation catalyzed by monooxygenase MonCI using a natural substrate analog.

Deng, Y.Guan, Y.Xiao, H.Kang, Y.Dang, D.Jiang, G.Wang, Q.Yang, Y.Cheng, L.Zang, Y.Zhang, S.He, W.Hotta, K.Liu, J.Q.Yang, Z.Chen, X.

(2025) Int J Biol Macromol 311: 142876-142876

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.142876
  • Primary Citation of Related Structures:  
    9IWV, 9UDB, 9UDD, 9UDE

  • PubMed Abstract: 

    Monensin, a polyether antibiotic produced by Streptomyces cinnamonensis, is synthesized through a series of stereospecific epoxidations orchestrated by the FAD-dependent monooxygenase MonCI. This study presents the crystal structure of MonCI in complex with a substrate analog, farnesyl acetate, which undergoes in vitro epoxidation at all three olefinic sites by MonCI. Additionally, we have solved the crystal structures of MonCI in complex with mono- and bis-epoxide intermediates. Structural analysis revealed that the interactions between MonCI and its substrate are predominantly hydrophobic, with residue Y208 playing a crucial role in substrate translocation. Computational modeling emphasizes the importance of FAD proximity to each olefinic group for efficient catalysis, providing insight into the mechanistic pathways for the first, second, and third epoxidations. Notably, when combined with electrochemical techniques, the yield of tri-epoxide farnesyl acetate reached 94 %, surpassing traditional enzymatic catalysis. This work not only elucidates the catalytic mechanism of MonCI but also underscores its potential as an effective biocatalyst for processive epoxidation in organic synthesis.


  • Organizational Affiliation

    Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative epoxidase LasC
A, B
488Streptomyces lasalocidiMutation(s): 0 
Gene Names: lsd18lasC
EC: 1.14.13
UniProt
Find proteins for B5M9L6 (Streptomyces lasalocidi)
Explore B5M9L6 
Go to UniProtKB:  B5M9L6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5M9L6
Sequence Annotations
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  • 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 
C [auth A],
F [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ELY
Query on ELY
A, B
L-PEPTIDE LINKINGC10 H22 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.230 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.04α = 74.8
b = 61.97β = 81.86
c = 76.29γ = 76.8
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21807088

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Database references
  • Version 1.2: 2025-05-21
    Changes: Database references