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2fgp

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Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6

Structural highlights

2fgp is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

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.

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:16411744^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE. Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry. 2006 Jan 24;45(3):686-700. PMID:16411744 doi:10.1021/bi051887k

1 Structural highlights
2 Publication Abstract from PubMed
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2fgp"

Categories: Large Structures | Salter JD | Wedekind JE

@@ Line 1: / Line 1: @@
 ==Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6==
-<StructureSection load='2fgp' size='340' side='right' caption='[[2fgp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='2fgp' size='340' side='right'caption='[[2fgp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2fgp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FGP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FGP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fgp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FGP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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]] 2.4&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=N6G:((2R,3S,4R,5S)-5-(2,6-DIAMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL+DIHYDROGEN+PHOSPHATE'>N6G</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N6G:((2R,3S,4R,5S)-5-(2,6-DIAMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL+DIHYDROGEN+PHOSPHATE'>N6G</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zfr|1zfr]], [[1zft|1zft]], [[2bcz|2bcz]], [[1zfv|1zfv]], [[1zfx|1zfx]], [[2bcy|2bcy]]</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=2fgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fgp OCA], [https://pdbe.org/2fgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fgp RCSB], [https://www.ebi.ac.uk/pdbsum/2fgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fgp ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fgp OCA], [http://pdbe.org/2fgp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fgp RCSB], [http://www.ebi.ac.uk/pdbsum/2fgp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fgp ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 20: / Line 19: @@
 ==See Also==
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Salter, J D]]
+[[Category: Large Structures]]
-[[Category: Wedekind, J E]]
+[[Category: Salter JD]]
-[[Category: Diaminopurine]]
+[[Category: Wedekind JE]]
-[[Category: G8]]
-[[Category: In-line geometry]]
-[[Category: Mutant]]
-[[Category: Ribozyme]]
-[[Category: Rna]]

2fgp

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Current revision

Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6

Structural highlights

Publication Abstract from PubMed

See Also

References

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