1kse
From Proteopedia
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|PDB= 1kse |SIZE=350|CAPTION= <scene name='initialview01'>1kse</scene> | |PDB= 1kse |SIZE=350|CAPTION= <scene name='initialview01'>1kse</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=OXI:OXOLINIC ACID'>OXI</scene> | + | |LIGAND= <scene name='pdbligand=5AT:5'-AMINO-5'-DEOXYTHYMIDINE'>5AT</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=OXI:OXOLINIC+ACID'>OXI</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kse OCA], [http://www.ebi.ac.uk/pdbsum/1kse PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kse RCSB]</span> | ||
}} | }} | ||
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[[Category: Stitelman, D H.]] | [[Category: Stitelman, D H.]] | ||
[[Category: Tuma, J.]] | [[Category: Tuma, J.]] | ||
| - | [[Category: OXI]] | ||
[[Category: disrupted terminal basepair]] | [[Category: disrupted terminal basepair]] | ||
[[Category: dna]] | [[Category: dna]] | ||
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[[Category: synthetic hybrid]] | [[Category: synthetic hybrid]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:52:55 2008'' |
Revision as of 18:52, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Solution Structure of a quinolone-capped DNA duplex
Overview
Quinolones are gyrase inhibitors that are widely used as antibiotics in the clinic. When covalently attached to oligonucleotides as 5'-acylamido substituents, quinolones were found to stabilize duplexes of oligonucleotides against thermal denaturation. For short duplexes, such as qu-T*GCGCA, where qu is a quinolone residue and T is a 5'-amino-5'-deoxythymidine residue, an increase in the UV melting point of up to 27.8 degrees C was measured. The stabilizing effect was demonstrated for all quinolones tested, namely nalidixic acid, oxolinic acid, pipemidic acid, cinoxacin, norfloxacin, and ofloxacin. The three-dimensional structure of (oa-T*GCGCA)2, where oa is an oxolinic acid residue, was solved by two-dimensional NMR spectroscopy and restrained molecular dynamics. In this complex, the oxolinic acid residues disrupt the terminal T1:A6 base pairs and stack on the G2:C5 base pairs. The displaced adenosine residues bind in the minor groove of the core duplex, while the thymidine residues pack against the oxolinic acid residues. The "molecular cap" thus formed fits tightly on the G:C base pairs, resulting in increased base-pairing fidelity, as demonstrated in UV melting experiments with the sequence oa-T*GGTTGAC and target strands containing a mismatched nucleobase. The structure of the "molecular cap" with its disrupted terminal base pair may also be helpful for modeling how quinolones block re-ligation of DNA strands in the active site of gyrases.
About this Structure
1KSE is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
On the effect of covalently appended quinolones on termini of DNA duplexes., Tuma J, Connors WH, Stitelman DH, Richert C, J Am Chem Soc. 2002 Apr 24;124(16):4236-46. PMID:11960452
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