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| | == Structural highlights == | | == Structural highlights == |
| | <table><tr><td colspan='2'>[[3bbi]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BBI FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3bbi]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BBI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </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> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=MTU:9-BETA-D-RIBOFURANOSYL-9H-PURIN-2-AMINE'>MTU</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene></td></tr> | + | <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=MTU:9-BETA-D-RIBOFURANOSYL-9H-PURIN-2-AMINE'>MTU</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2p7f|2p7f]], [[3b58|3b58]], [[3b5a|3b5a]], [[3b5f|3b5f]], [[3b5s|3b5s]], [[3b91|3b91]], [[3bbk|3bbk]], [[3bbm|3bbm]]</div></td></tr>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbi OCA], [https://pdbe.org/3bbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bbi RCSB], [https://www.ebi.ac.uk/pdbsum/3bbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbi ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbi OCA], [https://pdbe.org/3bbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bbi RCSB], [https://www.ebi.ac.uk/pdbsum/3bbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbi ProSAT]</span></td></tr> |
| | </table> | | </table> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Krucinska, J]] | + | [[Category: Krucinska J]] |
| - | [[Category: MacElrevey, C]] | + | [[Category: MacElrevey C]] |
| - | [[Category: Wedekind, J E]] | + | [[Category: Wedekind JE]] |
| - | [[Category: 2'o-methyl]]
| + | |
| - | [[Category: 2-aminopurine]]
| + | |
| - | [[Category: Hairpin ribozyme]]
| + | |
| - | [[Category: Linker]]
| + | |
| - | [[Category: Phosphoryl transfer]]
| + | |
| - | [[Category: Rna]]
| + | |
| Structural highlights
3bbi is a 3 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.35Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
The hairpin ribozyme requires functional groups from Ade38 to achieve efficient bond cleavage or ligation. To identify molecular features that contribute to catalysis, structures of position 38 base variants 2,6-diaminopurine (DAP), 2-aminopurine (AP), cytosine (Cyt), and guanine (Gua) were determined between 2.2 and 2.8 A resolution. For each variant, two substrate modifications were compared: (1) a 2'-O-methyl-substituent at Ade-1 was used in lieu of the nucleophile to mimic the precatalytic state, and (2) a 3'-deoxy-2',5'-phosphodiester linkage between Ade-1 and Gua+1 was used to mimic a reaction-intermediate conformation. While the global fold of each variant remained intact, the results revealed the importance of Ade38 N1 and N6 groups. Absence of N6 resulting from AP38 coincided with failure to localize the precatalytic scissile phosphate. Cyt38 severely impaired catalysis in a prior study, and its structures here indicated an anti base conformation that sequesters the imino moiety from the scissile bond. Gua38 was shown to be even more deleterious to activity. Although the precatalytic structure was nominally affected, the reaction-intermediate conformation indicated a severe electrostatic clash between the Gua38 keto oxygen and the pro-Rp oxygen of the scissile bond. Overall, position 38 modifications solved in the presence of 2'-OMe Ade-1 deviated from in-line geometry, whereas variants with a 2',5' linkage exhibited S-turn destabilization, as well as base conformational changes from syn to anti. These findings demonstrate the importance of the Ade38 Watson-Crick face in attaining a reaction-intermediate state and the sensitivity of the RNA fold to restructuring when electrostatic and shape features fail to complement.
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.,MacElrevey C, Salter JD, Krucinska J, Wedekind JE RNA. 2008 Aug;14(8):1600-16. Epub 2008 Jul 2. PMID:18596253[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ MacElrevey C, Salter JD, Krucinska J, Wedekind JE. Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. RNA. 2008 Aug;14(8):1600-16. Epub 2008 Jul 2. PMID:18596253 doi:rna.1055308
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