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.


1yls

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:58, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yls.gif|left|200px]]
 
-
<!--
+
==Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene==
-
The line below this paragraph, containing "STRUCTURE_1yls", creates the "Structure Box" on the page.
+
<StructureSection load='1yls' size='340' side='right'caption='[[1yls]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1yls]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YLS FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSL:(D)-2-METHYLSELENYL-2-DEOXYCYTIDINE-5-PHOSPHATE'>CSL</scene>, <scene name='pdbligand=DAI:(3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1,2]-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE'>DAI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr>
-
{{STRUCTURE_1yls| PDB=1yls | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yls OCA], [https://pdbe.org/1yls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yls RCSB], [https://www.ebi.ac.uk/pdbsum/1yls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yls ProSAT]</span></td></tr>
 +
</table>
-
'''Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene'''
+
==See Also==
-
 
+
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The majority of structural efforts addressing RNA's catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a lambda-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions.
+
[[Category: Large Structures]]
-
 
+
[[Category: Dauter Z]]
-
==About this Structure==
+
[[Category: Hobartner C]]
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YLS OCA].
+
[[Category: Jaschke A]]
-
 
+
[[Category: Keiper S]]
-
==Reference==
+
[[Category: Malinina L]]
-
Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation., Serganov A, Keiper S, Malinina L, Tereshko V, Skripkin E, Hobartner C, Polonskaia A, Phan AT, Wombacher R, Micura R, Dauter Z, Jaschke A, Patel DJ, Nat Struct Mol Biol. 2005 Mar;12(3):218-24. Epub 2005 Feb 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15723077 15723077]
+
[[Category: Micura R]]
-
[[Category: Dauter, Z.]]
+
[[Category: Patel DJ]]
-
[[Category: Hobartner, C.]]
+
[[Category: Phan AT]]
-
[[Category: Jaschke, A.]]
+
[[Category: Polonskaia A]]
-
[[Category: Keiper, S.]]
+
[[Category: Serganov A]]
-
[[Category: Malinina, L.]]
+
[[Category: Skripkin E]]
-
[[Category: Micura, R.]]
+
[[Category: Tereshko V]]
-
[[Category: Patel, D J.]]
+
[[Category: Wombacher R]]
-
[[Category: Phan, A T.]]
+
-
[[Category: Polonskaia, A.]]
+
-
[[Category: Serganov, A.]]
+
-
[[Category: Skripkin, E.]]
+
-
[[Category: Tereshko, V.]]
+
-
[[Category: Wombacher, R.]]
+
-
[[Category: Carbon-carbon bond formation]]
+
-
[[Category: Catalytic mechanism]]
+
-
[[Category: Crystal structure]]
+
-
[[Category: Diels-alder reaction]]
+
-
[[Category: Ribozyme]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:29:14 2008''
+

Current revision

Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

PDB ID 1yls

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/1yls"
Personal tools