1yy0: Difference between revisions
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|PDB= 1yy0 |SIZE=350|CAPTION= <scene name='initialview01'>1yy0</scene>, resolution 3.20Å | |PDB= 1yy0 |SIZE=350|CAPTION= <scene name='initialview01'>1yy0</scene>, resolution 3.20Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=A5M:2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE'>A5M</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=M5M:2'-(N-ACETAMIDE)-CYTIDINE-5'-MONOPHOSPHATE'>M5M</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yy0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yy0 OCA], [http://www.ebi.ac.uk/pdbsum/1yy0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yy0 RCSB]</span> | |||
}} | }} | ||
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[[Category: Krahn, J M.]] | [[Category: Krahn, J M.]] | ||
[[Category: Weeks, K M.]] | [[Category: Weeks, K M.]] | ||
[[Category: 2'-amine]] | [[Category: 2'-amine]] | ||
[[Category: 2-amide]] | [[Category: 2-amide]] | ||
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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 Mon Mar 31 01:26:14 2008'' | ||
Revision as of 01:26, 31 March 2008
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| , resolution 3.20Å | |||||||
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| Ligands: | , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of an RNA duplex containing a 2'-amine substitution and a 2'-amide product produced by in-crystal acylation at a C-A mismatch
OverviewOverview
Ribose 2'-amine substitutions are broadly useful as structural probes in nucleic acids. In addition, structure-selective chemical reaction at 2'-amine groups is a robust technology for interrogating local nucleotide flexibility and conformational changes in RNA and DNA. We analyzed crystal structures for several RNA duplexes containing 2'-amino cytidine (C(N)) residues that form either C(N)-G base pairs or C(N)-A mismatches. The 2'-amine substitution is readily accommodated in an A-form RNA helix and thus differs from the C2'-endo conformation observed for free nucleosides. The 2'-amide product structure was visualized directly by acylating a C(N)-A mismatch in intact crystals and is also compatible with A-form geometry. To visualize conformations able to facilitate formation of the amide-forming transition state, in which the amine nucleophile carries a positive partial charge, we analyzed crystals of the C(N)-A duplex at pH 5, where the 2'-amine is protonated. The protonated amine moves to form a strong electrostatic interaction with the 3'-phosphodiester. Taken together with solution-phase experiments, 2'-amine acylation is likely facilitated by either of two transition states, both involving precise positioning of the adjacent 3'-phosphodiester group.
About this StructureAbout this Structure
1YY0 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA., Gherghe CM, Krahn JM, Weeks KM, J Am Chem Soc. 2005 Oct 5;127(39):13622-8. PMID:16190727
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