4RZM

Crystal structure of the Lsd19-lasalocid A complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis.

Wong, F.T.Hotta, K.Chen, X.Fang, M.Watanabe, K.Kim, C.Y.

(2015) J.Am.Chem.Soc. 137: 86-89

  • DOI: 10.1021/ja511374k

  • PubMed Abstract: 
  • Biosynthesis of some polyether natural products involves a kinetically disfavored epoxide-opening cyclic ether formation, a reaction termed anti-Baldwin cyclization. One such example is the biosynthesis of lasalocid A, an ionophore antibiotic polyeth ...

    Biosynthesis of some polyether natural products involves a kinetically disfavored epoxide-opening cyclic ether formation, a reaction termed anti-Baldwin cyclization. One such example is the biosynthesis of lasalocid A, an ionophore antibiotic polyether. During lasalocid A biosynthesis, an epoxide hydrolase, Lsd19, converts the bisepoxy polyketide intermediate into the tetrahydrofuranyl-tetrahydropyran product. We report the crystal structure of Lsd19 in complex with lasalocid A. The structure unambiguously shows that the C-terminal domain of Lsd19 catalyzes the intriguing anti-Baldwin cyclization. We propose a general mechanism for epoxide selection by ionophore polyether epoxide hydrolases.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore , 117543 Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epoxide hydrolase LasB
A, B
283Streptomyces lasaliensisMutation(s): 0 
Gene Names: lsd19 (lasB)
EC: 5.5.1.-
Find proteins for B6ZK72 (Streptomyces lasaliensis)
Go to UniProtKB:  B6ZK72
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LSD
Query on LSD

Download SDF File 
Download CCD File 
A, B
Lasalocid A
6-[(3R,4S,5S,7R)-7-{(2S,3S,5S)-5-ethyl-5-[(2R,5R,6S)-5-ethyl-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]-3-methyltetrahydrofuran-2-yl}-4-hydroxy-3,5-dimethyl-6-oxononyl]-2-hydroxy-3-methylbenzoic acid
C34 H54 O8
BBMULGJBVDDDNI-OWKLGTHSSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 140.140α = 90.00
b = 140.140β = 90.00
c = 198.480γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
MOLREPphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references