1ho6: Difference between revisions
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|PDB= 1ho6 |SIZE=350|CAPTION= <scene name='initialview01'>1ho6</scene> | |PDB= 1ho6 |SIZE=350|CAPTION= <scene name='initialview01'>1ho6</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5'-PHOSPHATE'>CAR</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>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GAO:GUANINE+ARABINOSE-5'-PHOSPHATE'>GAO</scene>, <scene name='pdbligand=UAR:URACIL+ARABINOSE-5'-PHOSPHATE'>UAR</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1fc8|1FC8]], [[1hoq|1HOQ]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ho6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ho6 OCA], [http://www.ebi.ac.uk/pdbsum/1ho6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ho6 RCSB]</span> | |||
}} | }} | ||
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[[Category: rna]] | [[Category: rna]] | ||
''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 21:08:17 2008'' | ||
Revision as of 21:08, 30 March 2008
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| Ligands: | , , , , , , , , | ||||||
| Related: | 1FC8, 1HOQ
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM
OverviewOverview
Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, knowledge of the structure of ANA/RNA hybrids may prove helpful in the design of future antisense oligonucleotide analogs. In this study, we have determined the NMR solution structures of ANA/RNA and DNA/RNA hairpin duplexes and compared them to the recently published structure of a 2'F-ANA/RNA hairpin duplex. We demonstrate here that the sugars of RNA nucleotides of the ANA/RNA hairpin stem adopt the C3'-endo (north, A-form) conformation, whereas those of the ANA strand adopt a 'rigid' O4'-endo (east) sugar pucker. The DNA strand of the DNA/RNA hairpin stem is flexible, but the average DNA/RNA hairpin structural parameters are close to the ANA/RNA and 2'F-ANA/RNA hairpin parameters. The minor groove width of ANA/RNA, 2'F-ANA/RNA and DNA/RNA helices is 9.0 +/- 0.5 A, a value that is intermediate between that of A- and B-form duplexes. These results rationalize the ability of ANA/RNA and 2'F-ANA/RNA hybrids to elicit RNase H activity.
About this StructureAbout this Structure
1HO6 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids., Denisov AY, Noronha AM, Wilds CJ, Trempe JF, Pon RT, Gehring K, Damha MJ, Nucleic Acids Res. 2001 Nov 1;29(21):4284-93. PMID:11691916
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