9CCR | pdb_00009ccr

Crystal structure of the EspE7 thioesterase mutant R35A from the esperamicin biosynthetic pathway at 1.6 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.203 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Functional and Structural Studies on the Esperamicin Thioesterase and Progress toward Understanding Enediyne Core Biosynthesis.

Hankore, E.D.Miller, M.D.Kosgei, A.J.Xu, W.Tan, K.Endres, M.Bhardwaj, M.Joachimiak, G.Joachimiak, A.Phillips Jr., G.N.Thorson, J.S.Van Lanen, S.G.

(2025) J Nat Prod 

  • DOI: https://doi.org/10.1021/acs.jnatprod.5c00660
  • Primary Citation of Related Structures:  
    9CCR

  • PubMed Abstract: 

    Enediynes are among the most potent antitumor and antibacterial natural products. Studies on their biosynthetic pathways have identified a shared, linear polyene precursor generated from an iterative type I polyketide synthase (PKSE) as the source of the enediyne warhead. A key step is the release of this polyene from the PKSE by a discrete thioesterase (TE). Here, we used X-ray crystallography, site-directed mutagenesis, and heterologous coexpression of PKSEs and TEs to elucidate how enediyne TEs mediate the production of the polyene. We solved the structure of wild-type EspE7 from esperamicin producer Actinomodura verrucosospora . The substrate binding pocket was also defined upon serendipitous cocrystallization of an EspE7 mutant with a fatty acyl-CoA ligand. Structural data and in vitro activity assays with EspE7 mutants provide strong evidence that Glu68 in EspE7 and the analogous Glu residue in other enediyne TEs functions as a key catalytic residue, thus supporting a hydrolysis mechanism for enediyne TEs that aligns with that of Pseudomonas sp. 4-HB-CoA TE. Furthermore, combinations of 9- and 10-membered enediyne PKSEs and TEs produced 1,3,5,7,9,11,13-pentadecaheptaene ( 1 ) as the major product. Thus, the data further support previous conclusions that 1 serves as the sole precursor for the biosynthesis of all enediyne cores.


  • Organizational Affiliation
    • Pharmaceutical Sciences Department, University of Kentucky, 789 South Limestone, Lexington, Kentucky 40506, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioesterase
A, B, C, D
180Actinomadura verrucososporaMutation(s): 1 
Gene Names: EspE7
UniProt
Find proteins for A0A2D0TCG5 (Actinomadura verrucosospora)
Explore A0A2D0TCG5 
Go to UniProtKB:  A0A2D0TCG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TCG5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DCC
Query on DCC

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
DODECYL-COA
C33 H58 N7 O17 P3 S
YMCXGHLSVALICC-GMHMEAMDSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.203 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.769α = 90
b = 90.055β = 90
c = 95.718γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
DIALSdata scaling
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM115261
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA217255
National Science Foundation (NSF, United States)United StatesSTC-1231306

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references