1m5o: Difference between revisions

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[[Image:1m5o.gif|left|200px]]


{{Structure
==Transition State Stabilization by a Catalytic RNA==
|PDB= 1m5o |SIZE=350|CAPTION= <scene name='initialview01'>1m5o</scene>, resolution 2.20&Aring;
<StructureSection load='1m5o' size='340' side='right'caption='[[1m5o]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
<table><tr><td colspan='2'>[[1m5o]] is a 6 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=1M5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M5O FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
|GENE= SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AVC:ADENOSINE-5-MONOPHOSPHATE-2,3-VANADATE'>AVC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
}}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5o OCA], [https://pdbe.org/1m5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5o RCSB], [https://www.ebi.ac.uk/pdbsum/1m5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5o ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m5/1m5o_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1m5o ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


'''Transition State Stabilization by a Catalytic RNA'''
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:12376595<ref>PMID:12376595</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1m5o" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
==About this Structure==
== References ==
1M5O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5O OCA].
<references/>
 
__TOC__
==Reference==
</StructureSection>
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://www.ncbi.nlm.nih.gov/pubmed/12376595 12376595]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Amare, A R.Ferre-D.]]
[[Category: Ferre-D'Amare AR]]
[[Category: Massey, A P.]]
[[Category: Massey AP]]
[[Category: Rupert, P B.]]
[[Category: Rupert PB]]
[[Category: Sigurdsson, S T.]]
[[Category: Sigurdsson ST]]
[[Category: CA]]
[[Category: catalytic rna]]
[[Category: hairpin ribozyme]]
[[Category: transition state mimic]]
[[Category: u1a rna binding protein]]
[[Category: vandate]]
 
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Retrieved from "https://proteopedia.org/1m5o"