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| | ==Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes== | | ==Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes== |
| - | <StructureSection load='2p6z' size='340' side='right' caption='[[2p6z]], [[Resolution|resolution]] 1.93Å' scene=''> | + | <StructureSection load='2p6z' size='340' side='right'caption='[[2p6z]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2p6z]] is a 2 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=2P6Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P6Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2p6z]] is a 2 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=2P6Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P6Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.93Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2p7s|2p7s]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=2p6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p6z OCA], [http://pdbe.org/2p6z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p6z RCSB], [http://www.ebi.ac.uk/pdbsum/2p6z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2p6z ProSAT]</span></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=2p6z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p6z OCA], [https://pdbe.org/2p6z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p6z RCSB], [https://www.ebi.ac.uk/pdbsum/2p6z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p6z ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AMPS2_LITPI AMPS2_LITPI] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p6/2p6z_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p6/2p6z_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: Singh, U P]] | + | [[Category: Lithobates pipiens]] |
| - | [[Category: Amphinase]] | + | [[Category: Singh UP]] |
| - | [[Category: Cytotoxic rnase]]
| + | |
| - | [[Category: Enzyme efficiency]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Substrate specificity]]
| + | |
| Structural highlights
Function
AMPS2_LITPI
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
Besides Onconase (ONC) and its V11/N20/R103-variant, oocytes of the Northern Leopard frog (Rana pipiens) contain another homologue of ribonuclease A, which we named Amphinase (Amph). Four variants (Amph-1-4) were isolated and sequenced, each 114 amino acid residues in length and N-glycosylated at two positions. Sequence identities (a) among the variants and (b) versus ONC are 86.8-99.1% and 38.2-40.0%, respectively. When compared with other amphibian ribonucleases, a typical pattern of cysteine residues is evident but the N-terminal pyroglutamate residue is replaced by a six-residue extension. Amph variants have relatively weak ribonucleolytic activity that is insensitive to human ribonuclease inhibitor protein (RI). Values of k(cat)/K(M) with hypersensitive fluorogenic substrates are 10(4) and 10(2)-fold lower than the maximum values exhibited by ribonuclease A and ONC, respectively, and there is little cytosine/uracil or adenine/guanine discrimination at the B(1) or B(2) subsites, respectively. Amph variants have cytotoxic activity toward A-253 carcinoma cells that requires intact ribonucleolytic activity. The glycan component has little or no influence over single-stranded RNA cleavage, RI evasion or cytotoxicity. The crystal structures of natural and recombinant Amph-2 (determined at 1.8 and 1.9 A resolution, respectively) reveal that the N terminus is unlikely to play a catalytic role (but an unusual alpha2-beta1 loop may do so) and the B(2) subsite is rudimentary. At the active site, structural features that may contribute to the enzyme's low ribonucleolytic activity are the fixture of Lys14 in an obstructive position, the accompanying ejection of Lys42, and a lack of constraints on the conformations of Lys42 and His107.
Enzymatic and structural characterisation of amphinase, a novel cytotoxic ribonuclease from Rana pipiens oocytes.,Singh UP, Ardelt W, Saxena SK, Holloway DE, Vidunas E, Lee HS, Saxena A, Shogen K, Acharya KR J Mol Biol. 2007 Aug 3;371(1):93-111. Epub 2007 May 10. PMID:17560606[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Singh UP, Ardelt W, Saxena SK, Holloway DE, Vidunas E, Lee HS, Saxena A, Shogen K, Acharya KR. Enzymatic and structural characterisation of amphinase, a novel cytotoxic ribonuclease from Rana pipiens oocytes. J Mol Biol. 2007 Aug 3;371(1):93-111. Epub 2007 May 10. PMID:17560606 doi:http://dx.doi.org/10.1016/j.jmb.2007.04.071
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