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.


1nuj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:59, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1nuj.gif|left|200px]]<br /><applet load="1nuj" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1nuj, resolution 1.80&Aring;" />
 
-
'''THE LEADZYME STRUCTURE BOUND TO MG(H20)6(II) AT 1.8 A RESOLUTION'''<br />
 
-
==Overview==
+
==THE LEADZYME STRUCTURE BOUND TO MG(H20)6(II) AT 1.8 A RESOLUTION==
-
The leadzyme is a small ribozyme, derived from in vitro selection, which catalyzes site specific, Pb(2+)-dependent RNA cleavage. Pb(2+) is required for activity; Mg(2+) inhibits activity, while many divalent and trivalent ions enhance it. The leadzyme structure consists of an RNA duplex interrupted by a trinucleotide bulge. Here, crystal structures determined to 1.8 A resolution, both with Mg(2+) as the sole divalent counterion and with Mg(2+) and Sr(2+) (which mimics Pb(2+) with respect to binding but not catalysis), reveal the metal ion interactions with both the ground state and precatalytic conformations of the leadzyme. Mg(H(2)O)(6)(2+) ions bridge complementary strands of the duplex at multiple locations by binding tandem purines of one RNA strand in the major groove. At one site, Mg(H(2)O)(6)(2+) ligates the phosphodiester backbone of the trinucleotide bulge in the ground state conformation, but not in the precatalytic conformation, suggesting (a) Mg(2+) may inhibit leadzyme activity by stabilizing the ground state and (b) metal ions which displace Mg(2+) from this site may activate the leadzyme. Binding of Sr(2+) to the presumed catalytic Pb(2+) site in the precatalytic leadzyme induces local structural changes in a manner that would facilitate alignment of the catalytic ribose 2'-hydroxyl with the scissile bond for cleavage. These data support a model wherein binding of a catalytic ion to a precatalytic conformation of the leadzyme, in conjunction with the flexibility of the trinucleotide bulge, may facilitate structural rearrangements around the scissle phosphodiester bond favoring configurations that allow bond cleavage.
+
<StructureSection load='1nuj' size='340' side='right'caption='[[1nuj]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1nuj]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NUJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NUJ FirstGlance]. <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]] 1.8&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1nuj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nuj OCA], [https://pdbe.org/1nuj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nuj RCSB], [https://www.ebi.ac.uk/pdbsum/1nuj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nuj ProSAT]</span></td></tr>
 +
</table>
-
==About this Structure==
+
==See Also==
-
1NUJ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NUJ OCA].
+
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation., Wedekind JE, McKay DB, Biochemistry. 2003 Aug 19;42(32):9554-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12911297 12911297]
+
[[Category: Large Structures]]
-
[[Category: Protein complex]]
+
[[Category: Mckay DB]]
-
[[Category: Mckay, D B.]]
+
[[Category: Wedekind JE]]
-
[[Category: Wedekind, J E.]]
+
-
[[Category: MG]]
+
-
[[Category: alternate conformation]]
+
-
[[Category: bulged nucleotides]]
+
-
[[Category: homopurine base pairs]]
+
-
[[Category: hydrated magnesium]]
+
-
[[Category: lead-dependent cleavage]]
+
-
[[Category: leadzyme]]
+
-
[[Category: mg(h20)62+]]
+
-
[[Category: pseudohelical packing]]
+
-
[[Category: ribozyme]]
+
-
[[Category: rna]]
+
-
[[Category: sticky ends]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:10:11 2008''
+

Current revision

THE LEADZYME STRUCTURE BOUND TO MG(H20)6(II) AT 1.8 A RESOLUTION

PDB ID 1nuj

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/1nuj"
Personal tools