3ed1

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Rice GID1 complexed with GA3

Structural highlights

3ed1 is a 6 chain structure with sequence from Oryza sativa Japonica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shimada A, Ueguchi-Tanaka M, Nakatsu T, Nakajima M, Naoe Y, Ohmiya H, Kato H, Matsuoka M. Structural basis for gibberellin recognition by its receptor GID1. Nature. 2008 Nov 27;456(7221):520-3. doi: 10.1038/nature07546. PMID:19037316 doi:http://dx.doi.org/10.1038/nature07546

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ed1"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ed1' size='340' side='right'caption='[[3ed1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ed1]] 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=3ED1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ED1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ed1]] 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=3ED1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ED1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA3:GIBBERELLIN+A3'>GA3</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ebl|3ebl]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA3:GIBBERELLIN+A3'>GA3</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='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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ed1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ed1 OCA], [https://pdbe.org/3ed1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ed1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ed1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ed1 ProSAT]</span></td></tr>
 </table>
 == 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Japanese rice]]
 [[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]]

3ed1

From Proteopedia

Current revision

Crystal Structure of Rice GID1 complexed with GA3

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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