This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1vc6

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:21, 4 April 2018

Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Product with C75U Mutaion, cleaved in Imidazole and Mg2+ solutions

Structural highlights

1vc6 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1drz, 1cx0, 1vbx, 1vby, 1vbz, 1vc0, 1sjf, 1vc5, 1vc7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

A conformational switch controls hepatitis delta virus ribozyme catalysis.,Ke A, Zhou K, Ding F, Cate JH, Doudna JA Nature. 2004 May 13;429(6988):201-5. PMID:15141216^[2]

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

References

↑ Lutz CS, Cooke C, O'Connor JP, Kobayashi R, Alwine JC. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. RNA. 1998 Dec;4(12):1493-9. PMID:9848648
↑ Ke A, Zhou K, Ding F, Cate JH, Doudna JA. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature. 2004 May 13;429(6988):201-5. PMID:15141216 doi:http://dx.doi.org/10.1038/nature02522

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vc6"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Product with C75U Mutaion, cleaved in Imidazole and Mg2+ solutions==
 <StructureSection load='1vc6' size='340' side='right' caption='[[1vc6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1drz|1drz]], [[1cx0|1cx0]], [[1vbx|1vbx]], [[1vby|1vby]], [[1vbz|1vbz]], [[1vc0|1vc0]], [[1sjf|1sjf]], [[1vc5|1vc5]], [[1vc7|1vc7]]</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=1vc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vc6 OCA], [http://pdbe.org/1vc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vc6 RCSB], [http://www.ebi.ac.uk/pdbsum/1vc6 PDBsum]</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=1vc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vc6 OCA], [http://pdbe.org/1vc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vc6 RCSB], [http://www.ebi.ac.uk/pdbsum/1vc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vc6 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/1vc6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/1vc6_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vc6 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

1vc6

From Proteopedia

Revision as of 07:21, 4 April 2018

Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Product with C75U Mutaion, cleaved in Imidazole and Mg2+ solutions

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox