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 

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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.

(2013) Angew Chem Int Ed Engl 

  • DOI: 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 ...

    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.

    Organizational Affiliation: 

    Center for Free Electron Laser Science (CFEL), Hamburg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative SAM-dependent methyltransferaseA,
C [auth B],
E [auth C],
G [auth D]		264Streptomyces lasalocidiMutation(s): 0 
Gene Names: ecm18, E4U91_36955
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EchinomycinB [auth E],
D [auth F],
F [auth G],
H		8Streptomyces echinatusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
QUI
Query on QUI
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
J [auth A],
Z [auth D]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
P [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
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K [auth A],
L [auth A],
T [auth C]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MVA
Query on MVA		B [auth E],
D [auth F],
F [auth G],
H		L-PEPTIDE LINKINGC6 H13 N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000491
Query on PRD_000491		B [auth E], D [auth F], F [auth G], HEchinomycinCyclic depsipeptide / Antibiotic Ligand Interaction
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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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