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| [[Image:1s1l.gif|left|200px]]<br /><applet load="1s1l" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1s1l, resolution 2.20Å" />
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| '''Influence of Groove Interactions on the Formation of DNA Holliday Junctions'''<br />
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| ==Overview== | | ==Influence of Groove Interactions on the Formation of DNA Holliday Junctions== |
| The inosine-containing sequence d(CCIGTACm(5)CGG) is shown to crystallize as a four-stranded DNA junction. This structure is nearly identical to the antiparallel junction formed by the parent d(CCGGTACm(5)()CGG) sequence [Vargason, J. M., and Ho, P. S. (2002) J. Biol. Chem. 277, 21041-21049] in terms of its conformational geometry, and inter- and intramolecular interactions within the DNA and between the DNA and solvent, even though the 2-amino group in the minor groove of the important G(3).m(5)C(8) base pair of the junction core trinucleotide (italicized) has been removed. In contrast, the analogous 2,6-diaminopurine sequence d(CCDGTACTGG) crystallizes as resolved duplex DNAs, just like its parent sequence d(CCAGTACTGG) [Hays, F. A., Vargason, J. M., and Ho, P. S. (2003) Biochemistry 42, 9586-9597]. These results demonstrate that it is not the presence or absence of the 2-amino group in the minor groove of the R(3).Y(8) base pair that specifies whether a sequence forms a junction, but the positions of the extracyclic amino and keto groups in the major groove. Finally, the study shows that the arms of the junction can accommodate perturbations to the B-DNA conformation of the stacked duplex arms associated with the loss of the 2-amino substituent, and that two hydrogen bonding interactions from the C(7) and Y(8) pyrimidine nucleotides to phosphate oxygens of the junction crossover specify the geometry of the Holliday junction.
| | <StructureSection load='1s1l' size='340' side='right'caption='[[1s1l]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1s1l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S1L FirstGlance]. <br> |
| 1S1L is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1L OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> |
| ==Reference== | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s1l OCA], [https://pdbe.org/1s1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s1l RCSB], [https://www.ebi.ac.uk/pdbsum/1s1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s1l ProSAT]</span></td></tr> |
| Influence of minor groove substituents on the structure of DNA Holliday junctions., Hays FA, Jones ZJ, Ho PS, Biochemistry. 2004 Aug 3;43(30):9813-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15274635 15274635]
| | </table> |
| [[Category: Protein complex]]
| | __TOC__ |
| [[Category: Hays, F A.]] | | </StructureSection> |
| [[Category: Ho, P S.]] | | [[Category: Large Structures]] |
| [[Category: Jones, Z J.]] | | [[Category: Hays FA]] |
| [[Category: dna four-way junction]]
| | [[Category: Ho PS]] |
| [[Category: holliday junction]]
| | [[Category: Jones ZJ]] |
| [[Category: inosine]] | |
| [[Category: major groove]] | |
| [[Category: minor groove]] | |
| [[Category: x-ray diffraction]] | |
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:56:59 2008''
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