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1m5p

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[[Image:1m5p.gif|left|200px]]<br /><applet load="1m5p" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1m5p, resolution 2.60&Aring;" />
 
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'''Transition State Stabilization by a Catalytic RNA'''<br />
 
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==Overview==
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==Transition State Stabilization by a Catalytic RNA==
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The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes.
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<StructureSection load='1m5p' size='340' side='right'caption='[[1m5p]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1m5p]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M5P FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CG:5-CHLORO-5-DEOXY-GUANOSINE'>5CG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1m5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5p OCA], [https://pdbe.org/1m5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5p RCSB], [https://www.ebi.ac.uk/pdbsum/1m5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5p ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m5/1m5p_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m5p ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1M5P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5P OCA].
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*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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==Reference==
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== References ==
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Transition state stabilization by a catalytic RNA., Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR, Science. 2002 Nov 15;298(5597):1421-4. Epub 2002 Oct 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12376595 12376595]
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Amare, A R.Ferre-D.]]
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[[Category: Ferre-D'Amare AR]]
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[[Category: Massey, A.]]
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[[Category: Massey A]]
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[[Category: Rupert, P B.]]
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[[Category: Rupert PB]]
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[[Category: Sigurdsson, S T.]]
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[[Category: Sigurdsson ST]]
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[[Category: CA]]
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[[Category: catalytic rna]]
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[[Category: cl5*]]
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[[Category: hairpin ribozyme]]
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[[Category: u1a rna binding protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:51:43 2008''
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Current revision

Transition State Stabilization by a Catalytic RNA

PDB ID 1m5p

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