2zsi: Difference between revisions

Latest revision as of 18:46, 20 September 2023

Structural basis of gibberellin(GA4)-induced DELLA recognition by the gibberellin receptor

Structural highlights

2zsi is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	GA4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GID1A_ARATH 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 gibberellin GA4, but has no affinity for the biologically inactive GAs. In response to GA, interacts with specific DELLA proteins, known as repressors of GA-induced growth, and targets them for degradation via proteasome. Seems to be required for GA signaling that controls root growth, seed germination, stem elongation and flower development. Partially redundant with GID1B and GID1C.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Gibberellins control a range of growth and developmental processes in higher plants and have been widely used in the agricultural industry. By binding to a nuclear receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), gibberellins regulate gene expression by promoting degradation of the transcriptional regulator DELLA proteins, including GIBBERELLIN INSENSITIVE (GAI). The precise manner in which GID1 discriminates and becomes activated by bioactive gibberellins for specific binding to DELLA proteins remains unclear. Here we present the crystal structure of a ternary complex of Arabidopsis thaliana GID1A, a bioactive gibberellin and the amino-terminal DELLA domain of GAI. In this complex, GID1A occludes gibberellin in a deep binding pocket covered by its N-terminal helical switch region, which in turn interacts with the DELLA domain containing DELLA, VHYNP and LExLE motifs. Our results establish a structural model of a plant hormone receptor that is distinct from the mechanism of the hormone perception and effector recognition of the known auxin receptors.

Gibberellin-induced DELLA recognition by the gibberellin receptor GID1.,Murase K, Hirano Y, Sun TP, Hakoshima T Nature. 2008 Nov 27;456(7221):459-63. PMID:19037309^[4]

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

References

↑ Nakajima M, Shimada A, Takashi Y, Kim YC, Park SH, Ueguchi-Tanaka M, Suzuki H, Katoh E, Iuchi S, Kobayashi M, Maeda T, Matsuoka M, Yamaguchi I. Identification and characterization of Arabidopsis gibberellin receptors. Plant J. 2006 Jun;46(5):880-9. PMID:16709201 doi:https://dx.doi.org/10.1111/j.1365-313X.2006.02748.x
↑ Griffiths J, Murase K, Rieu I, Zentella R, Zhang ZL, Powers SJ, Gong F, Phillips AL, Hedden P, Sun TP, Thomas SG. Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell. 2006 Dec;18(12):3399-414. Epub 2006 Dec 28. PMID:17194763 doi:https://dx.doi.org/10.1105/tpc.106.047415
↑ Iuchi S, Suzuki H, Kim YC, Iuchi A, Kuromori T, Ueguchi-Tanaka M, Asami T, Yamaguchi I, Matsuoka M, Kobayashi M, Nakajima M. Multiple loss-of-function of Arabidopsis gibberellin receptor AtGID1s completely shuts down a gibberellin signal. Plant J. 2007 Jun;50(6):958-66. Epub 2007 May 23. PMID:17521411 doi:https://dx.doi.org/10.1111/j.1365-313X.2007.03098.x
↑ Murase K, Hirano Y, Sun TP, Hakoshima T. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature. 2008 Nov 27;456(7221):459-63. PMID:19037309 doi:https://dx.doi.org/10.1038/nature07519

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Nakajima M, Shimada A, Takashi Y, Kim YC, Park SH, Ueguchi-Tanaka M, Suzuki H, Katoh E, Iuchi S, Kobayashi M, Maeda T, Matsuoka M, Yamaguchi I. Identification and characterization of Arabidopsis gibberellin receptors. Plant J. 2006 Jun;46(5):880-9. PMID:16709201 doi:https://dx.doi.org/10.1111/j.1365-313X.2006.02748.x

[2] Griffiths J, Murase K, Rieu I, Zentella R, Zhang ZL, Powers SJ, Gong F, Phillips AL, Hedden P, Sun TP, Thomas SG. Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell. 2006 Dec;18(12):3399-414. Epub 2006 Dec 28. PMID:17194763 doi:https://dx.doi.org/10.1105/tpc.106.047415

[3] Iuchi S, Suzuki H, Kim YC, Iuchi A, Kuromori T, Ueguchi-Tanaka M, Asami T, Yamaguchi I, Matsuoka M, Kobayashi M, Nakajima M. Multiple loss-of-function of Arabidopsis gibberellin receptor AtGID1s completely shuts down a gibberellin signal. Plant J. 2007 Jun;50(6):958-66. Epub 2007 May 23. PMID:17521411 doi:https://dx.doi.org/10.1111/j.1365-313X.2007.03098.x

[4] Murase K, Hirano Y, Sun TP, Hakoshima T. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature. 2008 Nov 27;456(7221):459-63. PMID:19037309 doi:https://dx.doi.org/10.1038/nature07519

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='2zsi' size='340' side='right'caption='[[2zsi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zsi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZSI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zsi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZSI 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></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]] 1.8&#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;'>[[2zsh|2zsh]]</div></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></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GAI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2zsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zsi OCA], [https://pdbe.org/2zsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zsi RCSB], [https://www.ebi.ac.uk/pdbsum/2zsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zsi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/GID1A_ARATH GID1A_ARATH]] 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 gibberellin GA4, but has no affinity for the biologically inactive GAs. In response to GA, interacts with specific DELLA proteins, known as repressors of GA-induced growth, and targets them for degradation via proteasome. Seems to be required for GA signaling that controls root growth, seed germination, stem elongation and flower development. Partially redundant with GID1B and GID1C.<ref>PMID:16709201</ref> <ref>PMID:17194763</ref> <ref>PMID:17521411</ref>  [[https://www.uniprot.org/uniprot/GAI_ARATH GAI_ARATH]] Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. No effect of the BOI proteins on its stability. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Positively regulates XERICO expression. In contrast to RGA, it is less sensitive to GA. Its activity is probably regulated by other phytohormones such as auxin and ethylene.<ref>PMID:11487693</ref> <ref>PMID:11606551</ref> <ref>PMID:11606552</ref> <ref>PMID:14973286</ref> <ref>PMID:15128937</ref> <ref>PMID:16034591</ref> <ref>PMID:17933900</ref> <ref>PMID:9389651</ref>
+[https://www.uniprot.org/uniprot/GID1A_ARATH GID1A_ARATH] 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 gibberellin GA4, but has no affinity for the biologically inactive GAs. In response to GA, interacts with specific DELLA proteins, known as repressors of GA-induced growth, and targets them for degradation via proteasome. Seems to be required for GA signaling that controls root growth, seed germination, stem elongation and flower development. Partially redundant with GID1B and GID1C.<ref>PMID:16709201</ref> <ref>PMID:17194763</ref> <ref>PMID:17521411</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Hakoshima, T]]
+[[Category: Hakoshima T]]
-[[Category: Hirano, Y]]
+[[Category: Hirano Y]]
-[[Category: Murase, K]]
+[[Category: Murase K]]
-[[Category: Sun, T P]]
+[[Category: Sun TP]]
-[[Category: Alpha/beta-hydrolase fold]]
-[[Category: Carboxyesterase family]]
-[[Category: Developmental protein]]
-[[Category: Gibberellin signaling pathway]]
-[[Category: Hormone receptor]]
-[[Category: Hydrolase]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Plant hormone receptor]]
-[[Category: Receptor]]
-[[Category: Repressor]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Ubl conjugation]]

2zsi: Difference between revisions

Latest revision as of 18:46, 20 September 2023

Structural basis of gibberellin(GA4)-induced DELLA recognition by the gibberellin receptor

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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