4fbh: Difference between revisions

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 ==Structure of RIP from barley seeds==
-<StructureSection load='4fbh' size='340' side='right' caption='[[4fbh]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='4fbh' size='340' side='right'caption='[[4fbh]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fbh]] is a 1 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=4FBH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FBH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fbh]] is a 1 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=4FBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FBH 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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fb9|4fb9]], [[4fba|4fba]], [[4fbb|4fbb]], [[4fbc|4fbc]]</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></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'>[https://proteopedia.org/fgij/fg.htm?mol=4fbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fbh OCA], [https://pdbe.org/4fbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fbh RCSB], [https://www.ebi.ac.uk/pdbsum/4fbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fbh ProSAT]</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=4fbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fbh OCA], [http://pdbe.org/4fbh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fbh RCSB], [http://www.ebi.ac.uk/pdbsum/4fbh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fbh ProSAT]</span></td></tr>
 </table>
 == 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;">
-== 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<ref>PMID:23090398</ref>
+==See Also==
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4fbh" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[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]]
-[[Category: Ribosome]]
-[[Category: Ribosome inactivating protein]]
-[[Category: Rrna n-glycosylase activity]]