2npz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:28, 3 April 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker==
==Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker==
-
<StructureSection load='2npz' size='340' side='right' caption='[[2npz]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
+
<StructureSection load='2npz' size='340' side='right'caption='[[2npz]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[2npz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NPZ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[2npz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NPZ FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=PDI:PHOSPHORIC+ACID+MONO-(3-HYDROXY-PROPYL)+ESTER'>PDI</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.35&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zfr|1zfr]], [[2npy|2npy]]</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=PDI:PHOSPHORIC+ACID+MONO-(3-HYDROXY-PROPYL)+ESTER'>PDI</scene></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2npz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2npz RCSB], [http://www.ebi.ac.uk/pdbsum/2npz PDBsum]</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=2npz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npz OCA], [https://pdbe.org/2npz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2npz RCSB], [https://www.ebi.ac.uk/pdbsum/2npz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2npz ProSAT]</span></td></tr>
-
<table>
+
</table>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The hairpin ribozyme is a small catalytic RNA comprising two helix-loop-helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5'-U to form an intermolecular U.U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 A resolution or better. In contrast, C3L variants diffracted to 3.35 A and exhibited a 15 A expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6(1) contacts, which comprise numerous backbone to 2'-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.
+
-
 
+
-
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.,MacElrevey C, Spitale RC, Krucinska J, Wedekind JE Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):812-25. Epub 2007, Jun 15. PMID:17582172<ref>PMID:17582172</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
-
*[[Ribozyme|Ribozyme]]
+
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Krucinska, J.]]
+
[[Category: Large Structures]]
-
[[Category: MacElrevey, C.]]
+
[[Category: Krucinska J]]
-
[[Category: Wedekind, J E.]]
+
[[Category: MacElrevey C]]
-
[[Category: E loop]]
+
[[Category: Wedekind JE]]
-
[[Category: Hairpin]]
+
-
[[Category: Propyl]]
+
-
[[Category: Ribozyme]]
+
-
[[Category: Rna]]
+
-
[[Category: S turn]]
+

Current revision

Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker

PDB ID 2npz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2npz"
Personal tools