4RZM

Crystal structure of the Lsd19-lasalocid A complex

• PDB DOI: https://doi.org/10.2210/pdb4RZM/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces lasalocidi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-22 Released: 2015-01-21 
• Deposition Author(s): Mathews, I.I., Hotta, K., Chen, X., Kim, C.-Y.

---

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 

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

• PubMed: 25535803 
• DOI: https://doi.org/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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.92 kDa 
• Atom Count: 4,502 
• Modelled Residue Count: 557 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase LasB	A, B	283	Streptomyces lasalocidi	Mutation(s): 0  Gene Names: lasB, lsd19 EC: 5.5.1
UniProt
Find proteins for B6ZK72 (Streptomyces lasalocidi) Explore B6ZK72  Go to UniProtKB:  B6ZK72

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LSD	C [auth A], I [auth B]	Lasalocid A C34 H54 O8 BBMULGJBVDDDNI-OWKLGTHSSA-N
GOL	D [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	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
CL	R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A], P [auth B], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 140.14	α = 90
b = 140.14	β = 90
c = 198.48	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Mathews, I.I., Hotta, K., Chen, X., Kim, C.-Y.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description