1ykq
From Proteopedia
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|PDB= 1ykq |SIZE=350|CAPTION= <scene name='initialview01'>1ykq</scene>, resolution 3.5Å | |PDB= 1ykq |SIZE=350|CAPTION= <scene name='initialview01'>1ykq</scene>, resolution 3.5Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1ykv|1YKV]], [[1yls|1YLS]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ykq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ykq OCA], [http://www.ebi.ac.uk/pdbsum/1ykq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ykq RCSB]</span> | ||
}} | }} | ||
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[[Category: Tereshko, V.]] | [[Category: Tereshko, V.]] | ||
[[Category: Wombacher, R.]] | [[Category: Wombacher, R.]] | ||
| - | [[Category: CD]] | ||
| - | [[Category: MG]] | ||
[[Category: carbon-carbon bond]] | [[Category: carbon-carbon bond]] | ||
[[Category: catalytic mechanism]] | [[Category: catalytic mechanism]] | ||
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[[Category: rna crystal structure]] | [[Category: rna crystal structure]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:11:05 2008'' |
Revision as of 22:11, 30 March 2008
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| , resolution 3.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Related: | 1YKV, 1YLS
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of Diels-Alder ribozyme
Overview
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.
About this Structure
1YKQ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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:15723077
Page seeded by OCA on Mon Mar 31 01:11:05 2008
Categories: Protein complex | Dauter, Z. | Hobartner, C. | Jaschke, A. | Keiper, S. | Malinina, L. | Micura, R. | Patel, D J. | Phan, A T. | Polonskaia, A. | Serganov, A. | Skripkin, E. | Tereshko, V. | Wombacher, R. | Carbon-carbon bond | Catalytic mechanism | Diels-alder reaction | Ribozyme | Rna crystal structure
