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PDBsum entry 1l1v
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protein dna_rna links
DNA/antibiotic PDB id
1l1v

 

 

 

 

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Contents
Protein chain
11 a.a.
DNA/RNA
PDB id:
1l1v
Name: DNA/antibiotic
Title: Unusual actd/dna_ta complex structure
Structure: 5'-d( Gp Tp Cp Ap Cp Cp Gp Ap C)-3'. Chain: a. Engineered: yes. Actinomycin d. Chain: b. Synonym: dactinomycin. Engineered: yes
Source: Synthetic: yes. Streptomyces antibioticus. Organism_taxid: 1890
NMR struc: 6 models
Authors: S.-H.Chou,K.-H.Chin,F.-M.Chen
Key ref:
S.H.Chou et al. (2002). Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding. Proc Natl Acad Sci U S A, 99, 6625-6630. PubMed id: 12011426 DOI: 10.1073/pnas.102580399
Date:
20-Feb-02     Release date:   06-Mar-02    
PROCHECK
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 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 11 a.a.
Key:    Secondary structure

DNA/RNA chain
  G-T-C-A-C-C-G-A-C 9 bases

 

 
DOI no: 10.1073/pnas.102580399 Proc Natl Acad Sci U S A 99:6625-6630 (2002)
PubMed id: 12011426  
 
 
Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.
S.H.Chou, K.H.Chin, F.M.Chen.
 
  ABSTRACT  
 
Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The structure of actinomycin D. 		Figure 5.
Fig. 5. Space-filling structures of the classic ActD/5'-(GC)/(CG)-5' complex (Left) and the ActD/5'-(GGC)/(CCG)-5' (Right) complex. The color scheme used is the same as that in Fig. 4. The coordinates for the ActD/5'-(GC)/(CG)-5' complex are taken from Liu et al. (6). The views into the minor groove are shown in Top, whereas the down-to-the-helical views are shown in Bottom. The extra hydrophobic contact region between the ActD and DNA in the minor groove is indicated by a blue arrow.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19387499 C.Olano, C.Méndez, and J.A.Salas (2009).
Antitumor compounds from actinomycetes: from gene clusters to new derivatives by combinatorial biosynthesis.
  Nat Prod Rep, 26, 628-660.  
17659366 S.D.Stojanović, V.B.Medaković, G.Predović, M.Beljanski, and S.D.Zarić (2007).
XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins.
  J Biol Inorg Chem, 12, 1063-1071.  
16807967 H.K.Liu, F.Wang, J.A.Parkinson, J.Bella, and P.J.Sadler (2006).
Ruthenation of duplex and single-stranded d(CGGCCG) by organometallic anticancer complexes.
  Chemistry, 12, 6151-6165.  
15805595 E.Alexopoulos, E.A.Jares-Erijman, T.M.Jovin, R.Klement, R.Machinek, G.M.Sheldrick, and I.Usón (2005).
Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT).
  Acta Crystallogr D Biol Crystallogr, 61, 407-415.
PDB codes: 1unj 1unm
14715925 F.M.Chen, F.Sha, K.H.Chin, and S.H.Chou (2004).
The nature of actinomycin D binding to d(AACCAXYG) sequence motifs.
  Nucleic Acids Res, 32, 271-277.  
12524296 F.M.Chen, F.Sha, K.H.Chin, and S.H.Chou (2003).
Binding of actinomycin D to single-stranded DNA of sequence motifs d(TGTCT(n)G) and d(TGT(n)GTCT).
  Biophys J, 84, 432-439.  
12853642 F.M.Chen, F.Sha, K.H.Chin, and S.H.Chou (2003).
Unique actinomycin D binding to self-complementary d(CXYGGCCY'X'G) sequences: duplex disruption and binding to a nominally base-paired hairpin.
  Nucleic Acids Res, 31, 4238-4246.  
12736312 K.H.Chin, F.M.Chen, and S.H.Chou (2003).
Solution structure of the ActD-5'-CCGTT3GTGG-3' complex: drug interaction with tandem G.T mismatches and hairpin loop backbone.
  Nucleic Acids Res, 31, 2622-2629.
PDB code: 1ovf
12736295 S.H.Chou, K.H.Chin, and A.H.Wang (2003).
Unusual DNA duplex and hairpin motifs.
  Nucleic Acids Res, 31, 2461-2474.  
12433994 M.H.Hou, H.Robinson, Y.G.Gao, and A.H.Wang (2002).
Crystal structure of actinomycin D bound to the CTG triplet repeat sequences linked to neurological diseases.
  Nucleic Acids Res, 30, 4910-4917.
PDB code: 1mnv
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 codes are shown on the right.

 

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