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| | ==Crystal structure of onconase double mutant with spontaneously-assembled (AMP) 4 stack== | | ==Crystal structure of onconase double mutant with spontaneously-assembled (AMP) 4 stack== |
| - | <StructureSection load='2gmk' size='340' side='right' caption='[[2gmk]], [[Resolution|resolution]] 1.65Å' scene=''> | + | <StructureSection load='2gmk' size='340' side='right'caption='[[2gmk]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2gmk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Litpi Litpi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GMK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2gmk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lithobates_pipiens Lithobates pipiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GMK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RNP30_RANPI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8404 LITPI])</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=2gmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gmk OCA], [https://pdbe.org/2gmk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gmk RCSB], [https://www.ebi.ac.uk/pdbsum/2gmk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gmk ProSAT], [https://www.topsan.org/Proteins/CESG/2gmk TOPSAN]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gmk OCA], [http://pdbe.org/2gmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gmk RCSB], [http://www.ebi.ac.uk/pdbsum/2gmk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gmk ProSAT], [http://www.topsan.org/Proteins/CESG/2gmk TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RNP30_RANPI RNP30_RANPI]] Basic protein with antiproliferative/cytotoxic activity against several tumor cell lines in vitro, as well as antitumor in vivo. It exhibits a ribonuclease-like activity against high molecular weight ribosomal RNA. | + | [https://www.uniprot.org/uniprot/RNP30_LITPI RNP30_LITPI] Basic protein with antiproliferative/cytotoxic activity against several tumor cell lines in vitro, as well as antitumor in vivo. It exhibits a ribonuclease-like activity against high molecular weight ribosomal RNA. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gm/2gmk_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gm/2gmk_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Litpi]] | + | [[Category: Large Structures]] |
| - | [[Category: Bae, E]] | + | [[Category: Lithobates pipiens]] |
| - | [[Category: Bingman, C A]] | + | [[Category: Bae E]] |
| - | [[Category: Bitto, E]] | + | [[Category: Bingman CA]] |
| - | [[Category: Structural genomic]] | + | [[Category: Bitto E]] |
| - | [[Category: Lee, J E]] | + | [[Category: Lee JE]] |
| - | [[Category: Phillips, G N]] | + | [[Category: Phillips Jr GN]] |
| - | [[Category: Raines, R T]] | + | [[Category: Raines RT]] |
| - | [[Category: Wesenberg, G E]] | + | [[Category: Wesenberg GE]] |
| - | [[Category: Anti-tumor]]
| + | |
| - | [[Category: Cesg]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Onconase]]
| + | |
| - | [[Category: P-30 protein]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Ribonuclease]]
| + | |
| Structural highlights
Function
RNP30_LITPI Basic protein with antiproliferative/cytotoxic activity against several tumor cell lines in vitro, as well as antitumor in vivo. It exhibits a ribonuclease-like activity against high molecular weight ribosomal RNA.
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
Onconase (ONC) is a homolog of bovine pancreatic ribonuclease (RNase A) from the frog Rana pipiens. ONC displays antitumoral activity and is in advanced clinical trials for the treatment of cancer. Here, we report the first atomic structures of ONC-nucleic acid complexes: a T89N/E91A ONC-5'-AMP complex at 1.65 A resolution and a wild-type ONC-d(AUGA) complex at 1.90 A resolution. The latter structure and site-directed mutagenesis were used to reveal the atomic basis for substrate recognition and turnover by ONC. The residues in ONC that are proximal to the scissile phosphodiester bond (His10, Lys31, and His97) and uracil nucleobase (Thr35, Asp67, and Phe98) are conserved from RNase A and serve to generate a similar bell-shaped pH versus k(cat)/K(M) profile for RNA cleavage. Glu91 of ONC forms two hydrogen bonds with the guanine nucleobase in d(AUGA), and Thr89 is in close proximity to that nucleobase. Installing a neutral or cationic residue at position 91 or an asparagine residue at position 89 virtually eliminated the 10(2)-fold guanine:adenine preference of ONC. A variant that combined such substitutions, T89N/E91A ONC, actually preferred adenine over guanine. In contrast, installing an arginine residue at position 91 increased the guanine preference and afforded an ONC variant with the highest known k(cat)/K(M) value. These data indicate that ONC discriminates between guanine and adenine by using Coulombic interactions and a network of hydrogen bonds. The structure of the ONC-d(AUGA) complex was also used to probe other aspects of catalysis. For example, the T5R substitution, designed to create a favorable Coulombic interaction between ONC and a phosphoryl group in RNA, increased ribonucleolytic activity by twofold. No variant, however, was more toxic to human cancer cells than wild-type ONC. Together, these findings provide a cynosure for understanding catalysis of RNA cleavage in a system of high medicinal relevance.
Structural basis for catalysis by onconase.,Lee JE, Bae E, Bingman CA, Phillips GN Jr, Raines RT J Mol Biol. 2008 Jan 4;375(1):165-77. Epub 2007 Oct 4. PMID:18001769[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lee JE, Bae E, Bingman CA, Phillips GN Jr, Raines RT. Structural basis for catalysis by onconase. J Mol Biol. 2008 Jan 4;375(1):165-77. Epub 2007 Oct 4. PMID:18001769 doi:10.1016/j.jmb.2007.09.089
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