4RZM | pdb_00004rzm

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 (Depositor), 0.209 (DCC)
R-Value Work:
0.177 (Depositor), 0.185 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 25535803 Search on PubMed
DOI: https://doi.org/10.1021/ja511374k
Primary Citation 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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B6ZK72
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LSD Query on LSD Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	Lasalocid A C₃₄ H₅₄ O₈ BBMULGJBVDDDNI-OWKLGTHSSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B]	H [auth A], P [auth B], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.207 (Depositor), 0.209 (DCC)
R-Value Work: 0.177 (Depositor), 0.185 (DCC)
R-Value Observed: 0.179 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-01-21

Deposition Author(s):

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
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

4RZM | pdb_00004rzm

Crystal structure of the Lsd19-lasalocid A complex

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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