2qim: Difference between revisions

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<StructureSection load='2qim' size='340' side='right'caption='[[2qim]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
<StructureSection load='2qim' size='340' side='right'caption='[[2qim]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2qim]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/European_yellow_lupine European yellow lupine]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QIM FirstGlance]. <br>
<table><tr><td colspan='2'>[[2qim]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lupinus_luteus Lupinus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QIM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZEA:(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL'>ZEA</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]] 1.35&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xdf|1xdf]], [[1icx|1icx]], [[1ifv|1ifv]], [[2flh|2flh]], [[1bv1|1bv1]], [[1fm4|1fm4]], [[1e09|1e09]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZEA:(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL'>ZEA</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pr10.2b, Ypr10.2b ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3873 European yellow lupine])</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=2qim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qim OCA], [https://pdbe.org/2qim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qim RCSB], [https://www.ebi.ac.uk/pdbsum/2qim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qim 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=2qim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qim OCA], [https://pdbe.org/2qim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qim RCSB], [https://www.ebi.ac.uk/pdbsum/2qim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qim ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/P102B_LUPLU P102B_LUPLU] Class II ribonuclease (RNase) (By similarity). Binds to several cytokinins including natural adenine-type (e.g. trans-zeatin and kinetin) and artificial urea-type (e.g. N,N'-diphenylurea and N-phenyl-N'-(2-chloro-4-pyridyl)urea) hormones (PubMed:18406424, PubMed:19220853, PubMed:29630775). Interacts with melatonin (PubMed:29630775).[UniProtKB:P52779]<ref>PMID:18406424</ref> <ref>PMID:19220853</ref> <ref>PMID:29630775</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qim ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qim ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Plant pathogenesis-related (PR) proteins of class 10 (PR-10) are small and cytosolic. The main feature of their three-dimensional structure is a large cavity between a seven-stranded antiparallel beta-sheet and a long C-terminal alpha-helix. Although PR-10 proteins are abundant in plants, their physiological role remains unknown. Recent data have indicated ligand binding as their possible biological function. The article describes the structure of a complex between a classic PR-10 protein (yellow lupine LlPR-10.2B) and the plant hormone, trans-zeatin. Previously, trans-zeatin binding has been reported in a structurally related cytokinin-specific binding protein, which has a distant sequence relation with classic PR-10 proteins. In the present 1.35 A resolution crystallographic model, three perfectly ordered zeatin molecules are found in the binding cavity of the protein. The fact that three zeatin molecules are bound by the protein when only a fourfold molar excess of the ligand was used indicates an unusual type of affinity for this ligand and suggests that LlPR-10.2B, and perhaps other PR-10 proteins as well, acts as a reservoir of cytokinin molecules in the aqueous environment of the cell.
Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin.,Fernandes H, Pasternak O, Bujacz G, Bujacz A, Sikorski MM, Jaskolski M J Mol Biol. 2008 May 16;378(5):1040-51. Epub 2008 Mar 19. PMID:18406424<ref>PMID:18406424</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2qim" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: European yellow lupine]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bujacz, A]]
[[Category: Lupinus luteus]]
[[Category: Bujacz, G]]
[[Category: Bujacz A]]
[[Category: Fernandes, H C]]
[[Category: Bujacz G]]
[[Category: Jaskolski, M]]
[[Category: Fernandes HC]]
[[Category: Pasternak, O]]
[[Category: Jaskolski M]]
[[Category: Sikorski, M M]]
[[Category: Pasternak O]]
[[Category: Allergen]]
[[Category: Sikorski MM]]
[[Category: Cytokinin]]
[[Category: Pathogenesis-related protein]]
[[Category: Plant hormone]]
[[Category: Plant protein]]
[[Category: Pr-10 protein]]
[[Category: Trans-zeatin]]
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