3ebl: Difference between revisions

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<StructureSection load='3ebl' size='340' side='right'caption='[[3ebl]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3ebl' size='340' side='right'caption='[[3ebl]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ebl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EBL FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ebl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EBL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA4:GIBBERELLIN+A4'>GA4</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.9&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GID1, Os05g0407500, LOC_Os05g33730, OJ1657_H11.10, P0040B10.6 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA4:GIBBERELLIN+A4'>GA4</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=3ebl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ebl OCA], [https://pdbe.org/3ebl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ebl RCSB], [https://www.ebi.ac.uk/pdbsum/3ebl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ebl 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=3ebl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ebl OCA], [https://pdbe.org/3ebl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ebl RCSB], [https://www.ebi.ac.uk/pdbsum/3ebl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ebl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/GID1_ORYSJ GID1_ORYSJ]] Functions as soluble gibberellin (GA) receptor. GA is an essential hormone that regulates growth and development in plants. Binds with high affinity the biologically active GAs such as GA1, GA3 and GA4, but has low or no affinity for the biologically inactive GAs. Upon GA-binding, it interacts with the DELLA protein SLR1, a repressor of GA signaling. This leads to SLR1 degradation by the proteasome, allowing the GA signaling pathway.  
[https://www.uniprot.org/uniprot/GID1_ORYSJ GID1_ORYSJ] Functions as soluble gibberellin (GA) receptor. GA is an essential hormone that regulates growth and development in plants. Binds with high affinity the biologically active GAs such as GA1, GA3 and GA4, but has low or no affinity for the biologically inactive GAs. Upon GA-binding, it interacts with the DELLA protein SLR1, a repressor of GA signaling. This leads to SLR1 degradation by the proteasome, allowing the GA signaling pathway.
== 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=3ebl 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=3ebl ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. A nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), has a primary structure similar to that of the hormone-sensitive lipases (HSLs). Here we analyse the crystal structure of Oryza sativa GID1 (OsGID1) bound with GA(4) and GA(3) at 1.9 A resolution. The overall structure of both complexes shows an alpha/beta-hydrolase fold similar to that of HSLs except for an amino-terminal lid. The GA-binding pocket corresponds to the substrate-binding site of HSLs. On the basis of the OsGID1 structure, we mutagenized important residues for GA binding and examined their binding activities. Almost all of them showed very little or no activity, confirming that the residues revealed by structural analysis are important for GA binding. The replacement of Ile 133 with Leu or Val-residues corresponding to those of the lycophyte Selaginella moellendorffii GID1s-caused an increase in the binding affinity for GA(34), a 2beta-hydroxylated GA(4). These observations indicate that GID1 originated from HSL and was further modified to have higher affinity and more strict selectivity for bioactive GAs by adapting the amino acids involved in GA binding in the course of plant evolution.
Structural basis for gibberellin recognition by its receptor GID1.,Shimada A, Ueguchi-Tanaka M, Nakatsu T, Nakajima M, Naoe Y, Ohmiya H, Kato H, Matsuoka M Nature. 2008 Nov 27;456(7221):520-3. doi: 10.1038/nature07546. PMID:19037316<ref>PMID:19037316</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ebl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Japanese rice]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Kato, H]]
[[Category: Oryza sativa Japonica Group]]
[[Category: Matsuoka, M]]
[[Category: Kato H]]
[[Category: Nakatsu, T]]
[[Category: Matsuoka M]]
[[Category: Shimada, A]]
[[Category: Nakatsu T]]
[[Category: Ueguchi-Tanaka, M]]
[[Category: Shimada A]]
[[Category: Alpha/beta hydrolase]]
[[Category: Ueguchi-Tanaka M]]
[[Category: Gibberellin signaling pathway]]
[[Category: Hydrolase]]
[[Category: Hydrolase receptor]]
[[Category: Lipase]]
[[Category: Nucleus]]
[[Category: Receptor]]
Retrieved from "https://proteopedia.org/3ebl"