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 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4RZM

  • 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 polyether. During lasalocid A biosynthesis, an epoxide hydrolase, Lsd19, converts the bisepoxy polyketide intermediate into the tetrahydrofuranyl-tetrahydropyran product ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epoxide hydrolase LasBA, B283Streptomyces lasalocidiMutation(s): 0 
Gene Names: lasBlsd19
EC: 5.5.1
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LSD
Query on LSD

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
Lasalocid A
C34 H54 O8
BBMULGJBVDDDNI-OWKLGTHSSA-N
 Ligand Interaction
GOL
Query on GOL

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D [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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R [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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H [auth A],
P [auth B],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-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 
  • R-Value Observed: 0.179 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.14α = 90
b = 140.14β = 90
c = 198.48γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata 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: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references