|
|
| (11 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:1yzd.gif|left|200px]] | |
| | | | |
| - | {{Structure
| + | ==Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair== |
| - | |PDB= 1yzd |SIZE=350|CAPTION= <scene name='initialview01'>1yzd</scene>, resolution 2.35Å
| + | <StructureSection load='1yzd' size='340' side='right'caption='[[1yzd]], [[Resolution|resolution]] 2.35Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |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=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[1yzd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YZD FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5M:2-AMINE-CYTIDINE-5-MONOPHOSPHATE'>A5M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yzd OCA], [https://pdbe.org/1yzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yzd RCSB], [https://www.ebi.ac.uk/pdbsum/1yzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yzd ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1yrm|1YRM]], [[1yy0|1YY0]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yzd OCA], [http://www.ebi.ac.uk/pdbsum/1yzd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yzd RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair'''
| + | [[Category: Gherghe CM]] |
| - | | + | [[Category: Krahn JM]] |
| - | | + | [[Category: Weeks KM]] |
| - | ==Overview==
| + | |
| - | 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 Structure==
| + | |
| - | 1YZD is a [[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=1YZD OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/16190727 16190727]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Gherghe, C M.]] | + | |
| - | [[Category: Krahn, J M.]] | + | |
| - | [[Category: Weeks, K M.]] | + | |
| - | [[Category: 2'-amine]]
| + | |
| - | [[Category: duplex]]
| + | |
| - | [[Category: rna]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:26:50 2008''
| + | |
