|
|
| (11 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:2oue.gif|left|200px]] | |
| | | | |
| - | {{Structure
| + | ==Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution== |
| - | |PDB= 2oue |SIZE=350|CAPTION= <scene name='initialview01'>2oue</scene>, resolution 2.05Å
| + | <StructureSection load='2oue' size='340' side='right'caption='[[2oue]], [[Resolution|resolution]] 2.05Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=A2M:2'-O-METHYL-ADENOSINE-5'-MONOPHOSPHATE'>A2M</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[2oue]] is a 4 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1zfr 1zfr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OUE 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]] 2.05Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2oue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oue OCA], [https://pdbe.org/2oue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oue RCSB], [https://www.ebi.ac.uk/pdbsum/2oue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oue ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1zfx|1ZFX]], [[1zfv|1ZFV]], [[1zft|1ZFT]], [[2bcy|2BCY]], [[2fgp|2FGP]], [[2bcz|2BCZ]], [[1x9k|1X9K]], [[1x9c|1X9C]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oue OCA], [http://www.ebi.ac.uk/pdbsum/2oue PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2oue RCSB]</span>
| + | |
| - | }}
| + | |
| | | | |
| - | '''Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution'''
| + | ==See Also== |
| - | | + | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | The hairpin ribozyme requires functional group contributions from G8 to assist in phosphodiester bond cleavage. Previously, replacement of G8 by a series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on catalysis. To identify G8 features that contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were determined by X-ray crystallography in a resolution range between 2.3 and 2.7 A. For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution. The native structure revealed a scissile bond angle (tau) of 158 degrees, which is close to the requisite 180 degrees "in-line" geometry. Mutations G8(inosine), G8(diaminopurine), G8(aminopurine), G8(adenosine), and G8(uridine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees to 93 degrees) that paralleled their diminished solution activities. A superposition ensemble of all structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resulting from perturbation of the chemical environment and provided a rationale for how the exocyclic amine of nucleobase 8 promotes productive, in-line geometry. Changes at position 8 also caused variations in the A-1 sugar pucker. In this regard, variants A8 and U8 appeared to represent nonproductive ground states in which their 2'-OH groups mimicked the pro-R, nonbridging oxygen of the vanadate transition-state complex. Finally, the results indicated that ordered water molecules bind near the 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may play an important role in the reaction.
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Wedekind JE]] |
| - | ==About this Structure==
| + | |
| - | 2OUE is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. This structure supersedes the now removed PDB entry 1ZFR. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer., Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE, Biochemistry. 2006 Jan 24;45(3):686-700. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16411744 16411744]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Wedekind, J E.]] | + | |
| - | [[Category: all-rna]]
| + | |
| - | [[Category: catalytic rna]]
| + | |
| - | [[Category: e-loop]]
| + | |
| - | [[Category: hairpin ribozyme]]
| + | |
| - | [[Category: low salt]]
| + | |
| - | [[Category: mutation]]
| + | |
| - | [[Category: ribose zipper]]
| + | |
| - | [[Category: rna]]
| + | |
| - | [[Category: s-turn]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:23:13 2008''
| + | |
