2fjv: Difference between revisions
New page: left|200px<br /><applet load="2fjv" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fjv, resolution 2.05Å" /> '''RT29 Bound to D(CTTA... |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:2fjv.gif|left|200px]]<br /><applet load="2fjv" size=" | [[Image:2fjv.gif|left|200px]]<br /><applet load="2fjv" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2fjv, resolution 2.05Å" /> | caption="2fjv, resolution 2.05Å" /> | ||
'''RT29 Bound to D(CTTAATTCGAATTAAG) in complex with MMLV RT Catalytic Fragment'''<br /> | '''RT29 Bound to D(CTTAATTCGAATTAAG) in complex with MMLV RT Catalytic Fragment'''<br /> | ||
==Overview== | ==Overview== | ||
A general strategy for the rapid structural analysis of DNA binding | A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within approximately 3 days. Our application of the HT/HR strategy immediately revealed that RT29 has a preference for 4-base pair (bp), A.T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bp sites (such as ATTC) containing a G.C bp. On the basis of these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G.C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination. | ||
==About this Structure== | ==About this Structure== | ||
2FJV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Moloney_murine_leukemia_virus Moloney murine leukemia virus] with HXL as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] Full crystallographic information is available from [http:// | 2FJV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Moloney_murine_leukemia_virus Moloney murine leukemia virus] with <scene name='pdbligand=HXL:'>HXL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/RNA-directed_DNA_polymerase RNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.49 2.7.7.49] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJV OCA]. | ||
==Reference== | ==Reference== | ||
A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: | A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine., Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC, J Am Chem Soc. 2006 Jun 21;128(24):7846-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16771498 16771498] | ||
[[Category: Moloney murine leukemia virus]] | [[Category: Moloney murine leukemia virus]] | ||
[[Category: RNA-directed DNA polymerase]] | [[Category: RNA-directed DNA polymerase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Georgiadis, M | [[Category: Georgiadis, M M.]] | ||
[[Category: Goodwin, K | [[Category: Goodwin, K D.]] | ||
[[Category: HXL]] | [[Category: HXL]] | ||
[[Category: benzamidazole]] | [[Category: benzamidazole]] | ||
| Line 24: | Line 24: | ||
[[Category: water-mediated interaction]] | [[Category: water-mediated interaction]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:22:07 2008'' | ||
Revision as of 18:22, 21 February 2008
|
RT29 Bound to D(CTTAATTCGAATTAAG) in complex with MMLV RT Catalytic Fragment
OverviewOverview
A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within approximately 3 days. Our application of the HT/HR strategy immediately revealed that RT29 has a preference for 4-base pair (bp), A.T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bp sites (such as ATTC) containing a G.C bp. On the basis of these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G.C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination.
About this StructureAbout this Structure
2FJV is a Single protein structure of sequence from Moloney murine leukemia virus with as ligand. Active as RNA-directed DNA polymerase, with EC number 2.7.7.49 Full crystallographic information is available from OCA.
ReferenceReference
A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine., Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC, J Am Chem Soc. 2006 Jun 21;128(24):7846-54. PMID:16771498
Page seeded by OCA on Thu Feb 21 17:22:07 2008