2npy: Difference between revisions

Revision as of 09:45, 4 May 2008

Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1

OverviewOverview

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.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sun May 4 09:45:45 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:2npy.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2npy |SIZE=350|CAPTION= <scene name='initialview01'>2npy</scene>, resolution 2.65&Aring;
+The line below this paragraph, containing "STRUCTURE_2npy", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DU:2&#39;-DEOXYURIDINE-5&#39;-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=U2N:2&#39;-AMINO-2&#39;-DEOXYURIDINE+5&#39;-(DIHYDROGEN+PHOSPHATE)'>U2N</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2npy|  PDB=2npy  |  SCENE=  }}
-|RELATEDENTRY=[[1zfr|1ZFR]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2npy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npy OCA], [http://www.ebi.ac.uk/pdbsum/2npy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2npy RCSB]</span>
-}}
 '''Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1'''
@@ Line 19: / Line 16: @@
 ==About this Structure==
-NPY 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=2NPY OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPY OCA].
 ==Reference==
 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:[http://www.ncbi.nlm.nih.gov/pubmed/17582172 17582172]
-[[Category: Protein complex]]
 [[Category: Krucinska, J.]]
 [[Category: MacElrevey, C.]]
@@ Line 29: / Line 25: @@
 [[Category: 2'-deoxy 2'-amino]]
 [[Category: 9s linker]]
-[[Category: catalytic rna]]
+[[Category: Catalytic rna]]
-[[Category: e-loop]]
+[[Category: E-loop]]
-[[Category: hairpin ribozyme]]
+[[Category: Hairpin ribozyme]]
-[[Category: mutation]]
+[[Category: Mutation]]
-[[Category: ribose zipper]]
+[[Category: Ribose zipper]]
-[[Category: s-turn]]
+[[Category: S-turn]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 09:45:45 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:06:36 2008''