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| | ==Structure of mutant RIP from barley seeds== | | ==Structure of mutant RIP from barley seeds== |
| - | <StructureSection load='4fb9' size='340' side='right' caption='[[4fb9]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='4fb9' size='340' side='right'caption='[[4fb9]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fb9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FB9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FB9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fb9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FB9 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 1.75Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fba|4fba]], [[4fbb|4fbb]], [[4fbc|4fbc]], [[4fbh|4fbh]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RIP30 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4513 Hordeum vulgare])</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=4fb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fb9 OCA], [https://pdbe.org/4fb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fb9 RCSB], [https://www.ebi.ac.uk/pdbsum/4fb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fb9 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </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=4fb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fb9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fb9 RCSB], [http://www.ebi.ac.uk/pdbsum/4fb9 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RIP1_HORVU RIP1_HORVU] Inhibits the elongation phase of protein synthesis. It inactivates fungal ribosomes even more effectively than mammalian ribosomes and is thought to function as a constitutive antifungal agent in plants. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4fb9" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Hordeum vulgare]] | | [[Category: Hordeum vulgare]] |
| - | [[Category: RRNA N-glycosylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Kim, M K]] | + | [[Category: Kim MK]] |
| - | [[Category: Lee, B G]] | + | [[Category: Lee B-G]] |
| - | [[Category: Song, H K]] | + | [[Category: Song HK]] |
| - | [[Category: Suh, S W]] | + | [[Category: Suh SW]] |
| - | [[Category: Hydrolase]]
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| - | [[Category: Ribosome]]
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| - | [[Category: Ribosome inactivating protein]]
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| - | [[Category: Rrna n-glycosylase activity]]
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| Structural highlights
Function
RIP1_HORVU Inhibits the elongation phase of protein synthesis. It inactivates fungal ribosomes even more effectively than mammalian ribosomes and is thought to function as a constitutive antifungal agent in plants.
Publication Abstract from PubMed
Ribosome-inactivating protein (RIP), a defence protein found in various plants, possesses different chain architectures and activation mechanisms. The RIP from barley (bRIP) is a type I RIP and has sequence features that are divergent from those of type I and type II RIPs from dicotyledonous plants and even the type III RIP from maize. This study presents the first crystal structure of an RIP from a cereal crop, barley, in free, AMP-bound and adenine-bound states. For phasing, a codon-optimized synthetic brip1 gene was used and a vector was constructed to overexpress soluble bRIP fusion proteins; such expression has been verified in a number of cases. The overall structure of bRIP shows folding similar to that observed in other RIPs but also shows significant differences in specific regions, particularly in a switch region that undergoes a structural transition between a 3(10)-helix and a loop depending on the liganded state. The switch region is in a position equivalent to that of a proteolytically susceptible and putative ribosome-binding site in type III RIPs. Thus, the bRIP structure confirms the detailed enzymatic mechanism of this N-glycosidase and reveals a novel activation mechanism for type I RIPs from cereal crops.
Structures of the ribosome-inactivating protein from barley seeds reveal a unique activation mechanism.,Lee BG, Kim MK, Kim BW, Suh SW, Song HK Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1488-500. doi:, 10.1107/S0907444912037110. Epub 2012 Oct 13. PMID:23090398[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lee BG, Kim MK, Kim BW, Suh SW, Song HK. Structures of the ribosome-inactivating protein from barley seeds reveal a unique activation mechanism. Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1488-500. doi:, 10.1107/S0907444912037110. Epub 2012 Oct 13. PMID:23090398 doi:http://dx.doi.org/10.1107/S0907444912037110
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