2oj3: Difference between revisions

Revision as of 19:19, 21 February 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 with and as ligands. 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 Thu Feb 21 18:19:01 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]]<br />
+[[Image:2oj3.gif|left|200px]]<br /><applet load="2oj3" size="350" color="white" frame="true" align="right" spinBox="true"
-<applet load="2oj3" size="450" color="white" frame="true" align="right" spinBox="true"
 caption="2oj3, resolution 2.90&Aring;" />
 '''Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)'''<br />
 ==Overview==
-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.
+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 Structure==
-OJ3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with NCO and TL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2OJ3 OCA].
+OJ3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=NCO:'>NCO</scene> and <scene name='pdbligand=TL:'>TL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OJ3 OCA].
 ==Reference==
@@ Line 14: / Line 13: @@
 [[Category: Homo sapiens]]
 [[Category: Single protein]]
-[[Category: Batchelor, J.D.]]
+[[Category: Batchelor, J D.]]
 [[Category: Ding, F.]]
-[[Category: Doudna, J.A.]]
+[[Category: Doudna, J A.]]
 [[Category: Ke, A.]]
 [[Category: NCO]]
@@ Line 22: / Line 21: @@
 [[Category: tl+ and cobalt hexammine compete for binding sites.]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:11:48 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:19:01 2008''