1ldz

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[[Image:1ldz.gif|left|200px]]
 
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==SOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME, NMR, 25 STRUCTURES==
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The line below this paragraph, containing "STRUCTURE_1ldz", creates the "Structure Box" on the page.
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<StructureSection load='1ldz' size='340' side='right'caption='[[1ldz]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ldz]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LDZ FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ldz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ldz OCA], [https://pdbe.org/1ldz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ldz RCSB], [https://www.ebi.ac.uk/pdbsum/1ldz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ldz ProSAT]</span></td></tr>
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{{STRUCTURE_1ldz| PDB=1ldz | SCENE= }}
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The NMR solution structure of a lead-dependent ribozyme, known as the leadzyme, is presented. This ribozyme is among the smallest of the known catalytic RNAs, with an active site consisting of a six-nucleotide asymmetric internal loop. This loop has a roughly double-helical structure, including a protonated adenine-cytosine wobble base-pair, that positions the cytosine base 5' to the cleavage site in a double-helical conformation. The deviations from helical structure consist of two bulged guanosine residues, G7 and G9, where G7 is the residue 3' to the cleavage site. The scissile phosphate group of the leadzyme is not positioned for in-line nucleophilic attack. Therefore, a conformational rearrangement in the active site is required to reach the proposed transition state for this ribozyme. This is similar to previous observations in X-ray studies of the hammerhead ribozyme, and emphasizes the necessity for dynamic structural fluctuations in the catalytic mechanism of small ribozymes. A model for metal-binding in the leadzyme is proposed in which a lead ion binds to a bulged guanine base that is critical for leadzyme function.
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'''SOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME, NMR, 25 STRUCTURES'''
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NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis.,Hoogstraten CG, Legault P, Pardi A J Mol Biol. 1998 Nov 27;284(2):337-50. PMID:9813122<ref>PMID:9813122</ref>
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==Overview==
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The NMR solution structure of a lead-dependent ribozyme, known as the leadzyme, is presented. This ribozyme is among the smallest of the known catalytic RNAs, with an active site consisting of a six-nucleotide asymmetric internal loop. This loop has a roughly double-helical structure, including a protonated adenine-cytosine wobble base-pair, that positions the cytosine base 5' to the cleavage site in a double-helical conformation. The deviations from helical structure consist of two bulged guanosine residues, G7 and G9, where G7 is the residue 3' to the cleavage site. The scissile phosphate group of the leadzyme is not positioned for in-line nucleophilic attack. Therefore, a conformational rearrangement in the active site is required to reach the proposed transition state for this ribozyme. This is similar to previous observations in X-ray studies of the hammerhead ribozyme, and emphasizes the necessity for dynamic structural fluctuations in the catalytic mechanism of small ribozymes. A model for metal-binding in the leadzyme is proposed in which a lead ion binds to a bulged guanine base that is critical for leadzyme function.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDZ OCA].
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</div>
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<div class="pdbe-citations 1ldz" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis., Hoogstraten CG, Legault P, Pardi A, J Mol Biol. 1998 Nov 27;284(2):337-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9813122 9813122]
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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[[Category: Hoogstraten, C G.]]
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== References ==
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[[Category: Legault, P.]]
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<references/>
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[[Category: Pardi, A.]]
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__TOC__
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[[Category: Catalytic rna]]
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</StructureSection>
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[[Category: Internal loop]]
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[[Category: Large Structures]]
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[[Category: Leadzyme]]
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[[Category: Hoogstraten CG]]
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[[Category: Nmr spectroscopy]]
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[[Category: Legault P]]
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[[Category: Rna structure]]
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[[Category: Pardi A]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:49:49 2008''
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SOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME, NMR, 25 STRUCTURES

PDB ID 1ldz

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