1d63
From Proteopedia
(New page: 200px<br /><applet load="1d63" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d63, resolution 2.000Å" /> '''CRYSTAL STRUCTURE O...) |
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| - | [[Image:1d63.gif|left|200px]]<br /><applet load="1d63" size=" | + | [[Image:1d63.gif|left|200px]]<br /><applet load="1d63" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1d63, resolution 2.000Å" /> | caption="1d63, resolution 2.000Å" /> | ||
'''CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES'''<br /> | '''CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The AT-selective drug berenil has been co-crystallized with the | + | The AT-selective drug berenil has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The crystal structure has been solved to a resolution of 2.0 A and an R factor of 18.3%, with the location of 65 water molecules. The drug is symmetrically bound in the 5'-AATT region of the minor groove, with its amidinium groups hydrogen-bonding to O-2 atoms of the thymine base at each end of the binding site. This arrangement is distinct from that previously found for berenil with the sequence d(CGCGAATTCGCG)2, which has the drug bound to the sequencing 5'-ATT via hydrogen bonds to adenine N-3 atoms with the involvement of a bridging water molecule at one end of the binding site. The reasons for these differences are discussed in terms of changes in helical parameters; in particular propeller twist and base-pair roll are considered to be important. The conformational and base-pair geometry of the dodecanucleotide in the structure reported here, is closely similar to that for the native structure, suggesting that the 5'-AAATTT sequence does not significantly alter during drug binding, either because of its inflexibility or because its geometry is nearly ideal for berenil binding. |
==About this Structure== | ==About this Structure== | ||
| - | 1D63 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with BRN and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1D63 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=BRN:'>BRN</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D63 OCA]. |
==Reference== | ==Reference== | ||
Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features., Brown DG, Sanderson MR, Garman E, Neidle S, J Mol Biol. 1992 Jul 20;226(2):481-90. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1640462 1640462] | Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features., Brown DG, Sanderson MR, Garman E, Neidle S, J Mol Biol. 1992 Jul 20;226(2):481-90. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1640462 1640462] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Brown, D | + | [[Category: Brown, D G.]] |
[[Category: Garman, E.]] | [[Category: Garman, E.]] | ||
[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
| - | [[Category: Sanderson, M | + | [[Category: Sanderson, M R.]] |
[[Category: BRN]] | [[Category: BRN]] | ||
[[Category: MG]] | [[Category: MG]] | ||
| Line 22: | Line 22: | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:13:21 2008'' |
Revision as of 10:13, 21 February 2008
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CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES
Overview
The AT-selective drug berenil has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The crystal structure has been solved to a resolution of 2.0 A and an R factor of 18.3%, with the location of 65 water molecules. The drug is symmetrically bound in the 5'-AATT region of the minor groove, with its amidinium groups hydrogen-bonding to O-2 atoms of the thymine base at each end of the binding site. This arrangement is distinct from that previously found for berenil with the sequence d(CGCGAATTCGCG)2, which has the drug bound to the sequencing 5'-ATT via hydrogen bonds to adenine N-3 atoms with the involvement of a bridging water molecule at one end of the binding site. The reasons for these differences are discussed in terms of changes in helical parameters; in particular propeller twist and base-pair roll are considered to be important. The conformational and base-pair geometry of the dodecanucleotide in the structure reported here, is closely similar to that for the native structure, suggesting that the 5'-AAATTT sequence does not significantly alter during drug binding, either because of its inflexibility or because its geometry is nearly ideal for berenil binding.
About this Structure
1D63 is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features., Brown DG, Sanderson MR, Garman E, Neidle S, J Mol Biol. 1992 Jul 20;226(2):481-90. PMID:1640462
Page seeded by OCA on Thu Feb 21 12:13:21 2008
Categories: Protein complex | Brown, D G. | Garman, E. | Neidle, S. | Sanderson, M R. | BRN | MG | B-dna | Complexed with drug | Double helix
