8XU7 | pdb_00008xu7

Crystal structure of Lsd18 in complex with a product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

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


Literature

Structural Basis of Sequential Enantioselective Epoxidation by a Flavin-Dependent Monooxygenase in Lasalocid A Biosynthesis.

Wang, Q.Deng, Y.Viera, D.Liu, X.Liu, N.Hu, Y.Hu, X.Wei, H.Zhou, Q.Lan, T.He, W.Chen, X.Kim, C.Y.

(2025) Angew Chem Int Ed Engl 64: e202504982-e202504982

  • DOI: https://doi.org/10.1002/anie.202504982
  • Primary Citation of Related Structures:  
    8UP4, 8XTZ, 8XU7

  • PubMed Abstract: 

    Polyether polyketides are a structurally diverse group of natural products known for their antimicrobial and antiproliferative activities. Lasalocid A is a canonical natural polyether produced by the soil bacterium Streptomyces lasalocidi. In lasalocid A biosynthesis, a polyene polyketide intermediate is converted into a bisepoxide by the flavin-dependent monooxygenase enzyme Lsd18. Remarkably, Lsd18 acts on two distinct C═C groups in the substrate molecule, forming two (R,R) epoxides. We have determined the X-ray crystal structures of Lsd18 in the substrate-free, substrate-bound, and product-bound forms. Our work has revealed that Lsd18 has an extra-large substrate-binding pocket that allows the polyene to adopt different conformations within the enzyme pocket. This feature enables Lsd18 to epoxidate both of the C═C groups. Additionally, a subpocket located near the Lsd18 active site controls stereoselectivity by dictating which face of the C═C group is placed next to the flavin. Molecular understanding of how Lsd18 transforms a polyene into a bisepoxide during lasalocid A biosynthesis lays the foundation for the production of designer polyethers for drug development.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas, 79968, USA.


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
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 
C [auth A],
F [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
LSB (Subject of Investigation/LOI)
Query on LSB

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B]
(4R,5S)-3-((2R,3S,4S)-2-ethyl-5-((2R,3R)-2-ethyl-3-(2-((2R,3R)-2-ethyl-3-methyloxiran-2-yl)ethyl)oxiran-2-yl)-3-hydroxy-4-methylpentanoyl)-4-methyl-5-phenyloxazolidin-2-one
C29 H43 N O6
PLMSSXURLNIBST-CWZDORBJSA-N
CL
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: 2.20 Å
  • R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.037α = 74.79
b = 62.234β = 81.97
c = 76.294γ = 76.81
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata 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: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references
  • Version 1.2: 2025-06-18
    Changes: Database references