1m5p: Difference between revisions

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New page: left|200px<br /> <applet load="1m5p" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m5p, resolution 2.60Å" /> '''Transition State St...
 
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[[Image:1m5p.gif|left|200px]]<br />
<applet load="1m5p" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1m5p, resolution 2.60&Aring;" />
'''Transition State Stabilization by a Catalytic RNA'''<br />


==Overview==
==Transition State Stabilization by a Catalytic RNA==
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.
<StructureSection load='1m5p' size='340' side='right'caption='[[1m5p]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</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/m5/1m5p_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1m5p ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
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 CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M5P OCA].
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
==Reference==
== References ==
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]
<references/>
__TOC__
</StructureSection>
[[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.]]
[[Category: Massey A]]
[[Category: Rupert, P.B.]]
[[Category: Rupert PB]]
[[Category: Sigurdsson, S.T.]]
[[Category: Sigurdsson ST]]
[[Category: CA]]
[[Category: catalytic rna]]
[[Category: cl5*]]
[[Category: hairpin ribozyme]]
[[Category: u1a rna binding protein]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 18:07:48 2007''

Latest revision as of 10:40, 14 February 2024

Transition State Stabilization by a Catalytic RNATransition State Stabilization by a Catalytic RNA

Structural highlights

1m5p is a 8 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Lutz CS, Cooke C, O'Connor JP, Kobayashi R, Alwine JC. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. RNA. 1998 Dec;4(12):1493-9. PMID:9848648

1m5p, resolution 2.60Å

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