1jrv
From Proteopedia
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|PDB= 1jrv |SIZE=350|CAPTION= <scene name='initialview01'>1jrv</scene> | |PDB= 1jrv |SIZE=350|CAPTION= <scene name='initialview01'>1jrv</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <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=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1qsk|1QSK]], [[1jrw|1JRW]], [[1js5|1JS5]], [[1js7|1JS7]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jrv OCA], [http://www.ebi.ac.uk/pdbsum/1jrv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jrv RCSB]</span> | ||
}} | }} | ||
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[[Category: five-nucleotide bulge loop]] | [[Category: five-nucleotide bulge loop]] | ||
| - | ''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 21:38:07 2008'' |
Revision as of 18:38, 30 March 2008
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| Ligands: | , , , | ||||||
| Related: | 1QSK, 1JRW, 1JS5, 1JS7
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURE OF DAATAA DNA BULGE
Overview
The NMR structure analysis is described for two DNA molecules of identical stem sequences with a five base loop containing a pyrimidine, thymin or uracil, in between purines. These five unpaired nucleotides are bulged out and are known to induce a kink in the duplex structure. The dAATAA bulge DNA is kinked between the third and the fourth nucleotide. This contrasts with the previously studied dAAAAA bulge DNA where we found a kink between the fourth and fifth nucleotide. The total kinking angle is approximately 104 degrees for the dAATAA bulge. The findings were supported by electrophoretic data and fluorescence resonance energy transfer measurements of a similar DNA molecule end-labeled by suitable fluorescent dyes. For the dAAUAA bulge the NMR data result in a similar structure as reported for the dAATAA bulge with a kinking angle of approximately 87 degrees. The results are discussed in comparison with a rAAUAA RNA bulge found in a group I intron. Generally, the sequence-dependent structure of bulges is important to understand the role of DNA bulges in protein recognition.
About this Structure
1JRV is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of dAATAA and dAAUAA DNA bulges., Gollmick FA, Lorenz M, Dornberger U, von Langen J, Diekmann S, Fritzsche H, Nucleic Acids Res. 2002 Jun 15;30(12):2669-77. PMID:12060684
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