4NEC | pdb_00004nec

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

• PDB DOI: https://doi.org/10.2210/pdb4NEC/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Streptomyces lasalocidi, Streptomyces echinatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-29 Released: 2014-01-15 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.150 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: in silico

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

• PubMed: 24302672 
• DOI: https://doi.org/10.1002/anie.201307404
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.69 kDa 
• Atom Count: 8,028 
• Modeled Residue Count: 986 
• Deposited Residue Count: 1,088 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative SAM-dependent methyltransferase	A, C [auth B], E [auth C], G [auth D]	264	Streptomyces lasalocidi	Mutation(s): 0  Gene Names: ecm18
UniProt
Find proteins for Q0X0A7 (Streptomyces lasalocidi) Explore Q0X0A7  Go to UniProtKB:  Q0X0A7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Echinomycin	B [auth E], D [auth F], F [auth G], H	8	Streptomyces echinatus	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	X [auth D], Y [auth D]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
SAH	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	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	J [auth A], Z [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACT	P [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	K [auth A], L [auth A], T [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DSN	B [auth E], D [auth F], F [auth G], H	D-PEPTIDE LINKING	C3 H7 N O3		--
MVA	B [auth E], D [auth F], F [auth G], H	L-PEPTIDE LINKING	C6 H13 N O2		VAL
N2C	B [auth E], D [auth F], F [auth G], H	L-PEPTIDE LINKING	C5 H11 N O2 S		--
NCY	B [auth E], D [auth F], F [auth G], H	L-PEPTIDE LINKING	C4 H9 N O2 S		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000491	B [auth E], D [auth F], F [auth G], H	Echinomycin	Cyclic depsipeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.150 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.187	α = 90
b = 146.88	β = 102.63
c = 58.187	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
AMPLE	phasing
REFMAC	refinement
Aimless	data scaling
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): 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.

Revision History  

• 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