Crystal structure of trioxacarcin A covalently bound to DNA

Nucleic Acids Research

Volumn 36, Issue 10, 2008, Pages 3508-3514

  Pfoh, Roland ^a   Laatsch, Hartmut ^a   Sheldrick, George M ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; DOUBLE STRANDED DNA; GUANINE; GUTINGIMYCIN; NATURAL PRODUCT; OLIGONUCLEOTIDE; TRIOXACARCIN A; AMINOGLYCOSIDE; ANTIINFECTIVE AGENT; DNA; TRIOXACARCIN;

ALKYLATION; ARTICLE; CONTROLLED STUDY; COVALENT BOND; CRYSTAL STRUCTURE; DNA DRUG COMPLEX; DRUG DNA BINDING; DRUG DNA INTERACTION; DRUG STRUCTURE; INTERCALATION COMPLEX; PRIORITY JOURNAL; STEREOCHEMISTRY; X RAY DIFFRACTION; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; X RAY CRYSTALLOGRAPHY;

AMINOGLYCOSIDES; ANTI-BACTERIAL AGENTS; CRYSTALLOGRAPHY, X-RAY; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION;

EID: 45549101686     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn245     Document Type: Article

References (24)

1. Tomita,F., Tamaoki,T., Morimoto,M. and Fujimoto,K. (1981) Trioxacarcins, novel antitumor antibiotics. I. Producing organism, fermentation and biological activities. J. Antibiot., 34, 1519-1524.
2. Tamaoki,T., Shirahata,K., Iida,T. and Tomita,F. (1981) Trioxacarcins, novel antitumor antibiotics. II. Isolation, physicochemical properties and modes of action. J. Antibiot., 34, 1525-1530.
3. Maskey,R.P., Helmke,E., Kayser,O., Fiebig,H.H., Maier,A., Busche,A. and Laatsch,H. (2004) Anti-cancer and antibacterial trioxacarcins with high anti-malaria activity from a marine Streptomycete and their absolute stereochemistry. J. Antibiot., 57, 771-779.
4. Fitzner,A., Frauendorf,H., Laatsch,H. and Diederichsen,U. (2008) Formation of gutingimycin: Analytical investigations of trioxacarcin A mediated alkylation of dsDNA. Anal. Bioanal. Chem., 390, 1139-1147.
5. Maskey,R.P., Sevvana,M., Usón,I., Hehnke,E. and Laatsch,H. (2004) Gutingimycin: A highly complex metabolite from a marine streptomycete. Angew. Chem. Int. Ed., 43, 1281-1383.
6. Wang,A.H.-J., Ughetto,G., Quigley,G.J. and Rich,A. (1987) Interactions between an anthracycline antibiotic and DNA: Molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2Å resolution. Biochemistry, 26, 1152-1163.
7. Williams,L.D., Egli,M., Gao,Q., Bash,P., Marel,G.A., Boom,J.H., Rich,A. and Frederick,C.A. (1990) Structure of nogalamycin bound to a DNA hexamer. Proc. Natl Acad. Sci. USA, 87, 2225-2229.
8. Hansen,M.R. and Hurley,L.H. (1996) Pluramycins, old drugs having modern friends in structural biology. Acc. Chem. Res., 29, 249-258.
9. Hansen,M., Yun,S. and Hurley,L.H. (1995) Hedamycin intercalates the DNA helix and, through carbohydrate-mediated recognition in the minor groove, directs N7-alkylation of guanine in the major groove in a sequence-specific manner. Chem. Biol., 2, 229-240.
10. Sun,D., Hansen,M., Clement,J.J. and Hurley,L.H. (1993) Structure of the altromycin B (N7-guanine)-DNA adduct. A proposed prototypic DNA adduct structure for the pluramycin antitumor antibiotics. Biochemistry, 32, 8068-8074.
11. Hansen,M., Lee,S.-J., Cassady,J.M. and Hurley,L.H. (1996) Molecular details of the structure of a psorospermin-DNA covalent/intercalation complex and associated DNA sequence selectivity. J. Am. Chem. Soc. 118, 5553-5561.
12. Maskey,R.P., Helmke,E. and Laatsch,H. (2002) Parimycin: Isolation and structure elucidation of a novel cytotoxic 2,3-dihydroquinzarin analogue of γ-indomycinone from a marine streptomycete isolate. J. Antibiot. 55, 1031-1035.
13. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
14. Schneider,T.R. and Sheldrick,G.M. (2002) Substructure solution with SHELXD. Acta Crystallogr., D58, 1772-1779.
15. Sheldrick,G.M. (2002) Macromolecular phasing with SHELXE. Z. Kristallogr., 217, 644-650.
16. Emsley,P. and Cowtan,K. (2004) Coot: Model building tools for molecular graphics. Acta Crystallogr., D60, 2126-2132.
17. Murshudov,G.N., Vagin,A.A. and Dodson,E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr., D53, 240-255.
18. Lu,X.-J. and Olson,W.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
19. Schneider,B., Neidle,S. and Berman,H.M. (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers, 42, 113-124.
20. Olson,W.K., Bansal,M., Burley,S.K., Dickerson,R.E., Gerstein,M., Harvey,S.C., Heinemann,U., Lu,X.J., Neidle,S., Shakked,Z. et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol., 313, 219-237.
21. 2 by 2D NMR spectroscopy. Biochemistry, 35, 9314-9324.
22. Owen,E.A., Burley,G.A., Carver,J.A., Wickham,G. and Keniry,M.A. (2002) Structural investigation of the hedamycin d(ACCGGT) complex by NMR and restrained molecular dynamics. Biochem. Biophys. Res. Comm., 290, 1602-1608.
23. Collier,D.A., Neidle,S. and Brown,J.R. (1984) Molecular models for the interaction of the anti-tumor drug nogalamycin with DNA. Biochem. Pharmacol., 33, 2877-2880.
24. Parker,J.B., Bianchet,M.A., Krosky,D.J., Friedman,J.I., Amzel,L.M. and Stivers,J.T. (2007) Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature, 449, 433-437.