7D79

The structure of DcsB complex with its substrate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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

  • DOI: 10.1021/jacs.0c11226
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DltD domain-containing proteinB [auth A],
C [auth B],
D [auth C],
A [auth D]
322Beauveria bassiana ARSEF 2860Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ4WAT9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GY0 (Subject of Investigation/LOI)
Query on GY0

Download Ideal Coordinates CCD File 
I [auth D]methyl 3-[(E,3R,9R)-3,9-bis(oxidanyl)dec-4-enoyl]sulfanylpropanoate
C14 H24 O5 S
ALEAPVQZLMYNNX-BAEOLTKYSA-N
 Ligand Interaction
GYF (Subject of Investigation/LOI)
Query on GYF

Download Ideal Coordinates CCD File 
P [auth B]methyl 3-sulfanylpropanoate
C4 H8 O2 S
LDTLDBDUBGAEDT-UHFFFAOYSA-N
 Ligand Interaction
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
F [auth D],
G [auth D],
H [auth D],
M [auth A],
N [auth A],
F [auth D],
G [auth D],
H [auth D],
M [auth A],
N [auth A],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
E [auth D],
J [auth A],
K [auth A],
Q [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
S [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.263α = 84.846
b = 59.011β = 78.552
c = 113.99γ = 84.008
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release