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1de3

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(New page: 200px<br /><applet load="1de3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1de3" /> '''SOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCL...)
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[[Image:1de3.jpg|left|200px]]<br /><applet load="1de3" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1de3" />
 
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'''SOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN'''<br />
 
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==Overview==
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==SOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN==
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alpha-Sarcin selectively cleaves a single phosphodiester bond in a, universally conserved sequence of the major rRNA, that inactivates the, ribosome. The elucidation of the three-dimensional solution structure of, this 150 residue enzyme is a crucial step towards understanding, alpha-sarcin's conformational stability, ribonucleolytic activity, and its, exceptionally high level of specificity. Here, the solution structure has, been determined on the basis of 2658 conformationally relevant distances, restraints (including stereoespecific assignments) and 119 torsional, angular restraints, by nuclear magnetic resonance spectroscopy methods. A, total of 60 converged structures have been computed using the program, DYANA. The 47 best DYANA structures, following restrained energy, minimization by GROMOS, represent the solution structure of alpha-sarcin., The resulting average pairwise root-mean-square-deviation is 0.86 A for, backbone atoms and 1.47 A for all heavy atoms. When the more variable, regions are excluded from the analysis, the pairwise root-mean-square, deviation drops to 0.50 A and 1.00 A, for backbone and heavy atoms, respectively. The alpha-sarcin structure is similar to that reported for, restrictocin, although some differences are clearly evident, especially in, the loop regions. The average rmsd between the structurally aligned, backbones of the 47 final alpha-sarcin structures and the crystal, structure of restrictocin is 1.46 A. On the basis of a docking model, constructed with alpha-sarcin solution structure and the crystal structure, of a 29-nt RNA containing the sarcin/ricin domain, the regions in the, protein that could interact specifically with the substrate have been, identified. The structural elements that account for the specificity of, RNA recognition are located in two separate regions of the protein. One is, composed by residues 51 to 55 and loop 5, and the other region, located, more than 11 A away in the structure, is the positively charged segment, formed by residues 110 to 114.
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<StructureSection load='1de3' size='340' side='right'caption='[[1de3]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1de3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_giganteus Aspergillus giganteus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DE3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DE3 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">Solution NMR</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=1de3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1de3 OCA], [https://pdbe.org/1de3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1de3 RCSB], [https://www.ebi.ac.uk/pdbsum/1de3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1de3 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNAS_ASPGI RNAS_ASPGI] Alpha-sarcin is specific for purines in both single- and double-stranded RNA. Its toxic action on eukaryotic cells is the result of cleavage of a single phosphodiester bond in the 60S subunit of ribosomes.
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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/de/1de3_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=1de3 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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1DE3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_giganteus Aspergillus giganteus]. Active as [http://en.wikipedia.org/wiki/rRNA_endonuclease rRNA endonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.10 3.1.27.10] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DE3 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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The highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity., Perez-Canadillas JM, Santoro J, Campos-Olivas R, Lacadena J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M, J Mol Biol. 2000 Jun 16;299(4):1061-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10843858 10843858]
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[[Category: Aspergillus giganteus]]
[[Category: Aspergillus giganteus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: rRNA endonuclease]]
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[[Category: Bruix M]]
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[[Category: Bruix, M.]]
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[[Category: Campos-Olivas R]]
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[[Category: Campos-Olivas, R.]]
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[[Category: Gavilanes JG]]
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[[Category: Gavilanes, J.G.]]
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[[Category: Lacadena J]]
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[[Category: Lacadena, J.]]
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[[Category: Martinez del Pozo A]]
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[[Category: Perez-Canadillas, J.M.]]
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[[Category: Perez-Canadillas JM]]
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[[Category: Pozo, A.Martinez.del.]]
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[[Category: Rico M]]
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[[Category: Rico, M.]]
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[[Category: Santoro J]]
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[[Category: Santoro, J.]]
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[[Category: alpha-beta protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:12:34 2007''
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Current revision

SOLUTION STRUCTURE OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN

PDB ID 1de3

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