4NEC

Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Conversion of a disulfide bond into a thioacetal group during echinomycin biosynthesis.

Hotta, K.Keegan, R.M.Ranganathan, S.Fang, M.Bibby, J.Winn, M.D.Sato, M.Lian, M.Watanabe, K.Rigden, D.J.Kim, C.Y.

(2014) Angew Chem Int Ed Engl 53: 824-828

  • DOI: https://doi.org/10.1002/anie.201307404
  • Primary Citation of Related Structures:  
    4NEC

  • PubMed Abstract: 

    Echinomycin is a nonribosomal depsipeptide natural product with a range of interesting bioactivities that make it an important target for drug discovery and development. It contains a thioacetal bridge, a unique chemical motif derived from the disulfide bond of its precursor antibiotic triostin A by the action of an S-adenosyl-L-methionine-dependent methyltransferase, Ecm18. The crystal structure of Ecm18 in complex with its reaction products S-adenosyl-L-homocysteine and echinomycin was determined at 1.50 Å resolution. Phasing was achieved using a new molecular replacement package called AMPLE, which automatically derives search models from structure predictions based on ab initio protein modelling. Structural analysis indicates that a combination of proximity effects, medium effects, and catalysis by strain drives the unique transformation of the disulfide bond into the thioacetal linkage.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative SAM-dependent methyltransferaseA,
C [auth B],
E [auth C],
G [auth D]
264Streptomyces lasalocidiMutation(s): 0 
Gene Names: ecm18
UniProt
Find proteins for Q0X0A7 (Streptomyces lasalocidi)
Explore Q0X0A7 
Go to UniProtKB:  Q0X0A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0X0A7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EchinomycinB [auth E],
D [auth F],
F [auth G],
H
8Streptomyces echinatusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
X [auth D],
Y [auth D]
POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
SAH
Query on SAH

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I [auth A],
O [auth B],
S [auth C],
W [auth D]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
QUI
Query on QUI

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AA [auth H]
BA [auth H]
M [auth E]
N [auth E]
Q [auth F]
AA [auth H],
BA [auth H],
M [auth E],
N [auth E],
Q [auth F],
R [auth F],
U [auth G],
V [auth G]
2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
J [auth A],
Z [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACT
Query on ACT

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P [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

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K [auth A],
L [auth A],
T [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MVA
Query on MVA
B [auth E],
D [auth F],
F [auth G],
H
L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.187α = 90
b = 146.88β = 102.63
c = 58.187γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMPLEphasing
REFMACrefinement
Aimlessdata scaling
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Structure summary
  • Version 1.2: 2022-08-24
    Changes: Advisory, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Data collection, Derived calculations, Refinement description