3RGA | pdb_00003rga

Crystal structure of epoxide hydrolase for polyether lasalocid A biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.192 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis

Hotta, K.Chen, X.Paton, R.S.Minami, A.Li, H.Swaminathan, K.Mathews, I.I.Watanabe, K.Oikawa, H.Houk, K.N.Kim, C.-Y.

(2012) Nature 483: 355-358

  • DOI: https://doi.org/10.1038/nature10865
  • Primary Citation Related Structures: 
    3RGA

  • PubMed Abstract: 

    Polycyclic polyether natural products have fascinated chemists and biologists alike owing to their useful biological activity, highly complex structure and intriguing biosynthetic mechanisms. Following the original proposal for the polyepoxide origin of lasalocid and isolasalocid and the experimental determination of the origins of the oxygen and carbon atoms of both lasalocid and monensin, a unified stereochemical model for the biosynthesis of polyether ionophore antibiotics was proposed. The model was based on a cascade of nucleophilic ring closures of postulated polyepoxide substrates generated by stereospecific oxidation of all-trans polyene polyketide intermediates. Shortly thereafter, a related model was proposed for the biogenesis of marine ladder toxins, involving a series of nominally disfavoured anti-Baldwin, endo-tet epoxide-ring-opening reactions. Recently, we identified Lsd19 from the Streptomyces lasaliensis gene cluster as the epoxide hydrolase responsible for the epoxide-opening cyclization of bisepoxyprelasalocid A to form lasalocid A. Here we report the X-ray crystal structure of Lsd19 in complex with its substrate and product analogue to provide the first atomic structure-to our knowledge-of a natural enzyme capable of catalysing the disfavoured epoxide-opening cyclic ether formation. On the basis of our structural and computational studies, we propose a general mechanism for the enzymatic catalysis of polyether natural product biosynthesis.


  • Organizational Affiliation
    • National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, 117543 Singapore.

Macromolecule Content 

  • Total Structure Weight: 32 kDa 
  • Atom Count: 2,452 
  • Modeled Residue Count: 281 
  • Deposited Residue Count: 283 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epoxide hydrolase283Streptomyces lasalocidiMutation(s): 0 
Gene Names: lasBlsd19
EC: 3.3.2 (PDB Primary Data), 5.5.1 (UniProt)
UniProt
Find proteins for B6ZK72 (Streptomyces lasalocidi)
Explore B6ZK72 
Go to UniProtKB:  B6ZK72
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZK72
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LSB

Query on LSB



Download:Ideal Coordinates CCD File
B [auth A](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
ILD

Query on ILD



Download:Ideal Coordinates CCD File
C [auth A](4R,5S)-3-[(2R)-2-{(2S,2'R,4S,5S,5'R)-2,5'-diethyl-5'-[(1S)-1-hydroxyethyl]-4-methyloctahydro-2,2'-bifuran-5-yl}butanoyl]-4-methyl-5-phenyl-1,3-oxazolidin-2-one
C29 H43 N O6
SYWOXCFBKCIFEM-VTYWIBJUSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT

Query on FMT



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MOH

Query on MOH



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.192 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.85α = 90
b = 47.48β = 120.11
c = 62.33γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description