2oj3: Difference between revisions

Revision as of 11:01, 4 May 2008

Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)

OverviewOverview

The hepatitis delta virus (HDV) ribozyme catalyzes viral RNA self-cleavage through general acid-base chemistry in which an active-site cytidine and at least one metal ion are involved. Monovalent metal ions support slow catalysis and were proposed to substitute for structural, but not catalytic, divalent metal ions in the RNA. To investigate the role of monovalent cations in ribozyme structure and function, we determined the crystal structure of the precursor HDV ribozyme in the presence of thallium ions (Tl(+)). Two Tl(+) ions can occupy a previously observed divalent metal ion hexahydrate-binding site located near the scissile phosphate, but are easily competed away by cobalt hexammine, a magnesium hexahydrate mimic and potent reaction inhibitor. Intriguingly, a third Tl(+) ion forms direct inner-sphere contacts with the ribose 2'-OH nucleophile and the pro-S(p) scissile phosphate oxygen. We discuss possible structural and catalytic implications of monovalent cation binding for the HDV ribozyme mechanism.

About this StructureAbout this Structure

2OJ3 is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

ReferenceReference

Structural roles of monovalent cations in the HDV ribozyme., Ke A, Ding F, Batchelor JD, Doudna JA, Structure. 2007 Mar;15(3):281-7. PMID:17355864 Page seeded by OCA on Sun May 4 11:01:23 2008

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

OCA

@@ Line 1: / Line 1: @@
 [[Image:2oj3.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2oj3 |SIZE=350|CAPTION= <scene name='initialview01'>2oj3</scene>, resolution 2.90&Aring;
+The line below this paragraph, containing "STRUCTURE_2oj3", 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=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</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= SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+-->
-|DOMAIN=
+{{STRUCTURE_2oj3|  PDB=2oj3  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oj3 OCA], [http://www.ebi.ac.uk/pdbsum/2oj3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2oj3 RCSB]</span>
-}}
 '''Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)'''
@@ Line 29: / Line 26: @@
 [[Category: Doudna, J A.]]
 [[Category: Ke, A.]]
-[[Category: tl+ and cobalt hexammine compete for binding sites.]]
+[[Category: Tl+ and cobalt hexammine compete for binding sites.]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 11:01:23 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:18:34 2008''