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1m5k

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(New page: 200px<br /> <applet load="1m5k" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m5k, resolution 2.40&Aring;" /> '''CRYSTAL STRUCTURE O...)
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[[Image:1m5k.gif|left|200px]]<br />
 
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<applet load="1m5k" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1m5k, resolution 2.40&Aring;" />
 
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'''CRYSTAL STRUCTURE OF A HAIRPIN RIBOZYME IN THE CATALYTICALLY-ACTIVE CONFORMATION'''<br />
 
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==Overview==
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==Crystal structure of a hairpin ribozyme in the catalytically-active conformation==
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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.
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<StructureSection load='1m5k' size='340' side='right'caption='[[1m5k]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1m5k]] is a 6 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=1M5K 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]] 2.4&#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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</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=1m5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5k OCA], [https://pdbe.org/1m5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5k RCSB], [https://www.ebi.ac.uk/pdbsum/1m5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5k 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/m5/1m5k_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=1m5k 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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1M5K 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, CL, IOD and CH3 as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1HP6. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M5K 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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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11298439 11298439]
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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: Rupert, P.B.]]
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[[Category: Rupert PB]]
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[[Category: CA]]
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[[Category: CH3]]
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[[Category: CL]]
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[[Category: IOD]]
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[[Category: catalytic rna]]
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[[Category: hairpin ribozyme]]
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[[Category: substrate inhibitor strand]]
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[[Category: u1a rna binding protein docked conformation]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 18:07:39 2007''
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Current revision

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

PDB ID 1m5k

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