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| | ==Structure of mutant RIP from barley seeds in complex with adenine (AMP-incubated)== | | ==Structure of mutant RIP from barley seeds in complex with adenine (AMP-incubated)== |
| - | <StructureSection load='4fbb' size='340' side='right' caption='[[4fbb]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='4fbb' size='340' side='right'caption='[[4fbb]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fbb]] 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=4FBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FBB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fbb]] 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=4FBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FBB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fb9|4fb9]], [[4fba|4fba]], [[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=ADE:ADENINE'>ADE</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=4fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fbb OCA], [https://pdbe.org/4fbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fbb RCSB], [https://www.ebi.ac.uk/pdbsum/4fbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fbb 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>
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| - | <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=4fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fbb RCSB], [http://www.ebi.ac.uk/pdbsum/4fbb PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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;">
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| - | == Publication Abstract from PubMed ==
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| - | 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.
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| - | 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<ref>PMID:23090398</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | ==See Also== |
| - | </div>
| + | *[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]] |
| - | == References == | + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </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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