2d2l: Difference between revisions

Revision as of 08:19, 28 July 2008

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File:2d2l.png

Template:STRUCTURE 2d2l

Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39

Template:ABSTRACT PUBMED 16262240

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn., Alam S, Grum-Tokars V, Krucinska J, Kundracik ML, Wedekind JE, Biochemistry. 2005 Nov 8;44(44):14396-408. PMID:16262240

Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme., Grum-Tokars V, Milovanovic M, Wedekind JE, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):142-5. Epub 2002, Dec 19. PMID:12499551

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 {{STRUCTURE_2d2l|  PDB=2d2l  |  SCENE=  }}
-'''Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39'''
+===Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39===
-==Overview==
+<!--
-The hairpin ribozyme is an RNA enzyme that performs site-specific phosphodiester bond cleavage between nucleotides A-1 and G+1 within its cognate substrate. Previous functional studies revealed that the minimal hairpin ribozyme exhibited "gain-of-function" cleavage properties resulting from U39C or U39 to propyl linker (C3) modifications. Furthermore, each "mutant" displayed different magnesium-dependence in its activity. To investigate the molecular basis for these gain-of-function variants, crystal structures of minimal, junctionless hairpin ribozymes were solved in native (U39), and mutant U39C and U39(C3) forms. The results revealed an overall molecular architecture comprising two docked internal loop domains folded into a wishbone shape, whose tertiary interface forms a sequestered active site. All three minimal hairpin ribozymes bound Co(NH(3))(6)(3+) at G21/A40, the E-loop/S-turn boundary. The native structure also showed that U37 of the S-turn adopts both sequestered and exposed conformations that differ by a maximum displacement of 13 A. In the sequestered form, the U37 base packs against G36, and its 2'-hydroxyl group forms a water mediated hydrogen bond to O4' of G+1. These interactions were not observed in previous four-way-junction hairpin ribozyme structures due to crystal contacts with the U1A splicing protein. Interestingly, the U39C and U39(C3) mutations shifted the equilibrium conformation of U37 into the sequestered form through formation of new hydrogen bonds in the S-turn, proximal to the essential nucleotide A38. A comparison of all three new structures has implications for the catalytically relevant conformation of the S-turn and suggests a rationale for the distinctive metal dependence of each mutant.
+The line below this paragraph, {{ABSTRACT_PUBMED_16262240}}, adds the Publication Abstract to the page
+(as it appears on PubMed at http://www.pubmed.gov), where 16262240 is the PubMed ID number.
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+{{ABSTRACT_PUBMED_16262240}}
 ==About this Structure==
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 ==Reference==
 Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn., Alam S, Grum-Tokars V, Krucinska J, Kundracik ML, Wedekind JE, Biochemistry. 2005 Nov 8;44(44):14396-408. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16262240 16262240]
+Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme., Grum-Tokars V, Milovanovic M, Wedekind JE, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):142-5. Epub 2002, Dec 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12499551 12499551]
 [[Category: Alam, S.]]
 [[Category: Grum-Tokars, V.]]
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 [[Category: Propyl linker]]
 [[Category: Ribozyme]]
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