7D78 | pdb_00007d78

The structure of thioesterase DcsB

PDB DOI: https://doi.org/10.2210/pdb7D78/pdb

Classification: HYDROLASE
Organism(s): Beauveria bassiana ARSEF 2860
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-10-03 Released: 2021-01-27
Deposition Author(s): Tang, Y., Zhou, J.H., Wang, G.Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.183 (Depositor), 0.184 (DCC)
R-Value Work:
0.146 (Depositor), 0.148 (DCC)
R-Value Observed:
0.148 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A Polyketide Cyclase That Forms Medium-Ring Lactones.

Gao, D.W., Jamieson, C.S., Wang, G., Yan, Y., Zhou, J., Houk, K.N., Tang, Y.

(2021) J Am Chem Soc 143: 80-84

PubMed: 33351624 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.0c11226
Primary Citation Related Structures:
7D78, 7D79

PubMed Abstract:
Medium-ring lactones are synthetically challenging due to unfavorable energetics involved in cyclization. We have discovered a thioesterase enzyme DcsB, from the decarestrictine C1 ( 1 ) biosynthetic pathway, that efficiently performs medium-ring lactonizations. DcsB shows broad substrate promiscuity toward linear substrates that vary in lengths and substituents, and is a potential biocatalyst for lactonization. X-ray crystal structure and computational analyses provide insights into the molecular basis of catalysis.

Organizational Affiliation

State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content

Total Structure Weight: 70.78 kDa
Atom Count: 5,131
Modeled Residue Count: 592
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DltD domain-containing protein	A [auth D], B [auth A]	322	Beauveria bassiana ARSEF 2860	Mutation(s): 0 Gene Names: BBA_03809
UniProt
Find proteins for J4WAT9 (Beauveria bassiana (strain ARSEF 2860)) Explore J4WAT9 Go to UniProtKB: J4WAT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J4WAT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	D, G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D Focus chain G [auth A] Focus chain H [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain F [auth D] MOL2 format, chain E [auth D] MOL2 format, chain F [auth D] mmCIF format, chain E [auth D] mmCIF format, chain F [auth D]	E [auth D], F [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth D] Focus chain F [auth D] Interactions & Density Focus chain E [auth D] Focus chain F [auth D]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth D] MOL2 format, chain C [auth D] mmCIF format, chain C [auth D]	C [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth D] Interactions & Density Focus chain C [auth D]