1smx

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(New page: 200px<br /><applet load="1smx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1smx, resolution 1.80&Aring;" /> '''Crystal structure of...)
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[[Image:1smx.jpg|left|200px]]<br /><applet load="1smx" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1smx, resolution 1.80&Aring;" />
 
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'''Crystal structure of the S1 domain of RNase E from E. coli (native)'''<br />
 
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==Overview==
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==Crystal structure of the S1 domain of RNase E from E. coli (native)==
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S1 domains occur in four of the major enzymes of mRNA decay in Escherichia, coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the, structure of the S1 domain of RNase E, determined by both X-ray, crystallography and NMR spectroscopy. The RNase E S1 domain adopts an, OB-fold, very similar to that found with PNPase and the major cold shock, proteins, in which flexible loops are appended to a well-ordered, five-stranded beta-barrel core. Within the crystal lattice, the protein, forms a dimer stabilized primarily by intermolecular hydrophobic packing., Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1, domain undergoes a specific monomer-dimer equilibrium in solution with a, K(D) value in the millimolar range. The substitution of glycine 66 with, serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype, associated with this mutation in full-length RNase E. Based on amide, chemical shift perturbation mapping, the binding surface for a, single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a, groove of positive electrostatic potential containing several exposed, aromatic side-chains. This surface, which corresponds to the conserved, ligand-binding cleft found in numerous OB-fold proteins, lies distal to, the dimerization interface, such that two independent, oligonucleotide-binding sites can exist in the dimeric form of the RNase E, S1 domain. Based on these data, we propose that the S1 domain serves a, dual role of dimerization to aid in the formation of the tetrameric, quaternary structure of RNase E as described by Callaghan et al. in 2003, and of substrate binding to facilitate RNA hydrolysis by the adjacent, catalytic domains within this multimeric enzyme.
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<StructureSection load='1smx' size='340' side='right'caption='[[1smx]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1smx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SMX 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]] 1.8&#8491;</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=1smx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1smx OCA], [https://pdbe.org/1smx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1smx RCSB], [https://www.ebi.ac.uk/pdbsum/1smx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1smx ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
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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/sm/1smx_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=1smx 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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1SMX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1SMX OCA].
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces., Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP, J Mol Biol. 2004 Jul 30;341(1):37-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15312761 15312761]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cook, M.A.]]
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[[Category: Cook MA]]
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[[Category: Edge, R.E.]]
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[[Category: Edge RE]]
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[[Category: Lario, P.]]
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[[Category: Lario P]]
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[[Category: Mackie, G.A.]]
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[[Category: Mackie GA]]
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[[Category: McIntosh, L.P.]]
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[[Category: McIntosh LP]]
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[[Category: Schubert, M.]]
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[[Category: Schubert M]]
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[[Category: Strynadka, N.C.J.]]
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[[Category: Strynadka NCJ]]
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[[Category: ob-fold]]
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[[Category: rna-binding]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:30:07 2007''
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Current revision

Crystal structure of the S1 domain of RNase E from E. coli (native)

PDB ID 1smx

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