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[[Image:1m5k.png|left|200px]]
==Crystal structure of a hairpin ribozyme in the catalytically-active conformation==
<StructureSection load='1m5k' size='340' side='right' caption='[[1m5k]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1m5k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1hp6 1hp6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M5K FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1m5o|1m5o]], [[1m5p|1m5p]], [[1m5v|1m5v]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m5k RCSB], [http://www.ebi.ac.uk/pdbsum/1m5k PDBsum]</span></td></tr>
<table>
== 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/m5/1m5k_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems A and B. One strand of stem A harbours the scissile bond. The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribozyme aligns the 2'-OH nucleophile and the 5'-oxo leaving group by twisting apart the nucleotides that flank the scissile phosphate. The base of the nucleotide preceding the cleavage site is stacked within stem A; the next nucleotide, a conserved guanine, is extruded from stem A and accommodated by a highly complementary pocket in the minor groove of stem B. Metal ions are absent from the active site. The bases of four conserved purines are positioned potentially to serve as acid-base catalysts. This is the first structure determination of a fully assembled ribozyme active site that catalyses a phosphodiester cleavage without recourse to metal ions.


{{STRUCTURE_1m5k|  PDB=1m5k  |  SCENE=  }}
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis.,Rupert PB, Ferre-D'Amare AR Nature. 2001 Apr 12;410(6830):780-6. PMID:11298439<ref>PMID:11298439</ref>


===Crystal structure of a hairpin ribozyme in the catalytically-active conformation===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_11298439}}
 
==About this Structure==
[[1m5k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1hp6 1hp6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5K OCA].


==See Also==
==See Also==
*[[Hairpin Ribozyme|Hairpin Ribozyme]]
*[[Nucleoprotein|Nucleoprotein]]
*[[Nucleoprotein|Nucleoprotein]]
*[[Ribozyme|Ribozyme]]
*[[Ribozyme|Ribozyme]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:011298439</ref><ref group="xtra">PMID:012376595</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Amare, A R.Ferre-D.]]
[[Category: Amare, A R.Ferre-D.]]

Revision as of 21:21, 28 September 2014

Crystal structure of a hairpin ribozyme in the catalytically-active conformationCrystal structure of a hairpin ribozyme in the catalytically-active conformation

Structural highlights

1m5k is a 6 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 1hp6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:, ,
Related:1m5o, 1m5p, 1m5v
Gene:SNRPA (Homo sapiens)
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

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

Publication Abstract from PubMed

The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems A and B. One strand of stem A harbours the scissile bond. The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribozyme aligns the 2'-OH nucleophile and the 5'-oxo leaving group by twisting apart the nucleotides that flank the scissile phosphate. The base of the nucleotide preceding the cleavage site is stacked within stem A; the next nucleotide, a conserved guanine, is extruded from stem A and accommodated by a highly complementary pocket in the minor groove of stem B. Metal ions are absent from the active site. The bases of four conserved purines are positioned potentially to serve as acid-base catalysts. This is the first structure determination of a fully assembled ribozyme active site that catalyses a phosphodiester cleavage without recourse to metal ions.

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis.,Rupert PB, Ferre-D'Amare AR Nature. 2001 Apr 12;410(6830):780-6. PMID:11298439[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Rupert PB, Ferre-D'Amare AR. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature. 2001 Apr 12;410(6830):780-6. PMID:11298439 doi:10.1038/35071009

1m5k, resolution 2.40Å

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