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PDBsum entry 1vtg
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dna_rna ligands links
DNA/antibiotic PDB id
1vtg

 

 

 

 

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Contents
DNA/RNA
Ligands
DSN-ALA-NCY-MVA-
DSN-ALA-NCY-MVA
QUI ×2
PDB id:
1vtg
Name: DNA/antibiotic
Title: The molecular structure of a DNA-triostin a complex
Structure: DNA (5'-d( Cp Gp Tp Ap Cp G)-3'). Chain: a. Engineered: yes. Triostin a. Chain: b. Engineered: yes
Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Streptomyces sp.. Organism_taxid: 1931
Resolution:
1.67Å     R-factor:   0.189    
Authors: A.H.-J.Wang,G.Ughetto,G.J.Quigley,T.Hakoshima,G.A.Van Der Marel, J.H.Van Boom,A.Rich
Key ref: A.H.Wang et al. (1984). The molecular structure of a DNA-triostin A complex. Science, 225, 1115-1121. PubMed id: 6474168
Date:
18-Aug-88     Release date:   13-Jul-11    
 Headers
 References

DNA/RNA chain
  C-G-T-A-C-G 6 bases

 

 
Science 225:1115-1121 (1984)
PubMed id: 6474168  
 
 
The molecular structure of a DNA-triostin A complex.
A.H.Wang, G.Ughetto, G.J.Quigley, T.Hakoshima, G.A.van der Marel, J.H.van Boom, A.Rich.
 
  ABSTRACT  
 
The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG (C, cytosine; G, guanine; T, thymine; A, adenine). The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22259578 J.K.Harper, G.Strobel, and A.M.Arif (2012).
3-Carbamoylquinoxalin-1-ium chloride.
  Acta Crystallogr Sect E Struct Rep Online, 68, o79-o80.  
16552143 J.A.Cuesta-Seijo, M.S.Weiss, and G.M.Sheldrick (2006).
Serendipitous SAD phasing of an echinomycin-(ACGTACGT)2 bisintercalation complex.
  Acta Crystallogr D Biol Crystallogr, 62, 417-424.
PDB code: 2adw
15805599 J.A.Cuesta-Seijo, and G.M.Sheldrick (2005).
Structures of complexes between echinomycin and duplex DNA.
  Acta Crystallogr D Biol Crystallogr, 61, 442-448.
PDB codes: 1pfe 1xvk 1xvn 1xvr
10713522 H.L.Takusagawa, and F.Takusagawa (2000).
Crystallization and preliminary X-ray diffraction studies of d(ACGTAGCTACGT)2:[actinomycin D, (echinomycin)2] and d(ACGTAGCTACGT)2:[actinomycin D, (triostin A)2] complexes.
  Acta Crystallogr D Biol Crystallogr, 56, 344-347.  
10998231 X.L.Yang, H.Robinson, Y.G.Gao, and A.H.Wang (2000).
Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms.
  Biochemistry, 39, 10950-10957.
PDB codes: 1fd5 1fdg
9289011 H.Robinson, W.Priebe, J.B.Chaires, and A.H.Wang (1997).
Binding of two novel bisdaunorubicins to DNA studied by NMR spectroscopy.
  Biochemistry, 36, 8663-8670.
PDB codes: 1al9 1amd
8573569 C.Bailly, F.Hamy, and M.J.Waring (1996).
Cooperativity in the binding of echinomycin to DNA fragments containing closely spaced CpG sites.
  Biochemistry, 35, 1150-1161.  
8547242 M.C.Fletcher, and K.R.Fox (1996).
Dissociation kinetics of echinomycin from CpG binding sites in different sequence environments.
  Biochemistry, 35, 1064-1075.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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