5YTZ | pdb_00005ytz

Crystal structure of echinomycin-d(ACGTCGT)2 complex

• PDB DOI: https://doi.org/10.2210/pdb5YTZ/pdb
• NAKB: 5YTZ

• Classification: ANTIBIOTIC/DNA
• Organism(s): unidentified, Streptomyces echinatus
• Mutation(s): No 


• Deposited: 2017-11-20 Released: 2018-05-23 
• Deposition Author(s): Hou, M.H., Wu, P.C., Kao, Y.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex

Wu, P.C., Tzeng, S.L., Chang, C.K., Kao, Y.F., Waring, M.J., Hou, M.H.

(2018) Nucleic Acids Res 46: 7396-7404

• PubMed: 29741655 
• DOI: https://doi.org/10.1093/nar/gky345
• Primary Citation Related Structures: 
  5YTY, 5YTZ


• PubMed Abstract: 
  

  Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that the drug strongly prefers to bind to consecutive CpG steps separated by a single T:T mismatch. The preference appears to result from enhanced cooperativity associated with the binding of the second echinomycin molecule. Crystallographic studies reveal that this preference originates from the staggered quinoxaline rings of the two neighboring antibiotic molecules that surround the T:T mismatch forming continuous stacking interactions within the duplex. These and other associated changes in DNA conformation allow the formation of a minor groove pocket for tight binding of the second echinomycin molecule. We also show that echinomycin displays enhanced cytotoxicity against mismatch repair-deficient cell lines, raising the possibility of repurposing the drug for detection and treatment of mismatch repair-deficient cancers.

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Organizational Affiliation: 
• Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 40227, Taiwan.
Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan.
Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.
Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan.
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.82 kDa 
• Atom Count: 543 
• Modeled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3')	A, B	7	unidentified

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUI	G [auth D], H [auth D], J [auth F], K [auth F]	2-CARBOXYQUINOXALINE C9 H6 N2 O2 UPUZGXILYFKSGE-UHFFFAOYSA-N
MN	E [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	I [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DSN	C [auth D], D [auth F]	D-PEPTIDE LINKING	C3 H7 N O3		--
MVA	C [auth D], D [auth F]	L-PEPTIDE LINKING	C6 H13 N O2		VAL
N2C	C [auth D], D [auth F]	L-PEPTIDE LINKING	C5 H11 N O2 S		--
NCY	C [auth D], D [auth F]	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	C [auth D], D [auth F]	Echinomycin	Cyclic depsipeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.759	α = 90
b = 41.759	β = 90
c = 138.415	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Hou, M.H., Wu, P.C., Kao, Y.F.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2018-09-05
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description