8xas

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of AtARR1-DBD in complex with a DNA fragment

Structural highlights

8xas is a 10 chain structure with sequence from Arabidopsis thaliana and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.346Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARR1_ARATH Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins. Regulates SHY2 by binding to its promoter (PubMed:19039136). Involved in the root-meristem size determination through the regulation of cell differentiation (PubMed:17363254).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The phytohormone cytokinin has various roles in plant development, including meristem maintenance, vascular differentiation, leaf senescence, and regeneration. Prior investigations have revealed that cytokinin acts via a phosphorelay similar to the two-component system by which bacteria sense and respond to external stimuli. The eventual targets of this phosphorelay are type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs), containing the conserved N-terminal receiver domain (RD), middle DNA binding domain (DBD), and C-terminal transactivation domain. While it has been established for two decades that the phosphoryl transfer from a specific histidyl residue in ARABIDOPSIS HIS PHOSPHOTRANSFER PROTEINS (AHPs) to an aspartyl residue in the RD of B-ARRs results in a rapid transcriptional response to cytokinin, the underlying molecular basis remains unclear. In this work, we determine the crystal structures of the RD-DBD of ARR1 (ARR1(RD-DBD)) as well as the ARR1(DBD)-DNA complex from Arabidopsis. Analyses of the ARR1(DBD)-DNA complex have revealed the structural basis for sequence-specific recognition of the GAT trinucleotide by ARR1. In particular, comparing the ARR1(RD-DBD) and ARR1(DBD)-DNA structures reveals that unphosphorylated ARR1(RD-DBD) exists in a closed conformation with extensive contacts between the RD and DBD. In vitro and vivo functional assays have further suggested that phosphorylation of the RD weakens its interaction with DBD, subsequently permits the DNA binding capacity of DBD, and promotes the transcriptional activity of ARR1. Our findings thus provide mechanistic insights into phosphorelay activation of gene transcription in response to cytokinin.

The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin.,Zhou CM, Li JX, Zhang TQ, Xu ZG, Ma ML, Zhang P, Wang JW Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2319335121. doi: , 10.1073/pnas.2319335121. Epub 2024 Jan 10. PMID:38198526^[5]

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

References

↑ Hwang I, Sheen J. Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature. 2001 Sep 27;413(6854):383-9. PMID:11574878 doi:10.1038/35096500
↑ Sakai H, Honma T, Aoyama T, Sato S, Kato T, Tabata S, Oka A. ARR1, a transcription factor for genes immediately responsive to cytokinins. Science. 2001 Nov 16;294(5546):1519-21. PMID:11691951 doi:10.1126/science.1065201
↑ Dello Ioio R, Linhares FS, Scacchi E, Casamitjana-Martinez E, Heidstra R, Costantino P, Sabatini S. Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation. Curr Biol. 2007 Apr 17;17(8):678-82. PMID:17363254 doi:10.1016/j.cub.2007.02.047
↑ Dello Ioio R, Nakamura K, Moubayidin L, Perilli S, Taniguchi M, Morita MT, Aoyama T, Costantino P, Sabatini S. A genetic framework for the control of cell division and differentiation in the root meristem. Science. 2008 Nov 28;322(5906):1380-4. PMID:19039136 doi:10.1126/science.1164147
↑ Zhou CM, Li JX, Zhang TQ, Xu ZG, Ma ML, Zhang P, Wang JW. The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin. Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2319335121. PMID:38198526 doi:10.1073/pnas.2319335121

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8xas"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8xas is ON HOLD  until Paper Publication
+==Crystal structure of AtARR1-DBD in complex with a DNA fragment==
+<StructureSection load='8xas' size='340' side='right'caption='[[8xas]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8xas]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8XAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8XAS FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.346&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=8xas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8xas OCA], [https://pdbe.org/8xas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8xas RCSB], [https://www.ebi.ac.uk/pdbsum/8xas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8xas ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ARR1_ARATH ARR1_ARATH] Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins. Regulates SHY2 by binding to its promoter (PubMed:19039136). Involved in the root-meristem size determination through the regulation of cell differentiation (PubMed:17363254).<ref>PMID:11574878</ref> <ref>PMID:11691951</ref> <ref>PMID:17363254</ref> <ref>PMID:19039136</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The phytohormone cytokinin has various roles in plant development, including meristem maintenance, vascular differentiation, leaf senescence, and regeneration. Prior investigations have revealed that cytokinin acts via a phosphorelay similar to the two-component system by which bacteria sense and respond to external stimuli. The eventual targets of this phosphorelay are type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs), containing the conserved N-terminal receiver domain (RD), middle DNA binding domain (DBD), and C-terminal transactivation domain. While it has been established for two decades that the phosphoryl transfer from a specific histidyl residue in ARABIDOPSIS HIS PHOSPHOTRANSFER PROTEINS (AHPs) to an aspartyl residue in the RD of B-ARRs results in a rapid transcriptional response to cytokinin, the underlying molecular basis remains unclear. In this work, we determine the crystal structures of the RD-DBD of ARR1 (ARR1(RD-DBD)) as well as the ARR1(DBD)-DNA complex from Arabidopsis. Analyses of the ARR1(DBD)-DNA complex have revealed the structural basis for sequence-specific recognition of the GAT trinucleotide by ARR1. In particular, comparing the ARR1(RD-DBD) and ARR1(DBD)-DNA structures reveals that unphosphorylated ARR1(RD-DBD) exists in a closed conformation with extensive contacts between the RD and DBD. In vitro and vivo functional assays have further suggested that phosphorylation of the RD weakens its interaction with DBD, subsequently permits the DNA binding capacity of DBD, and promotes the transcriptional activity of ARR1. Our findings thus provide mechanistic insights into phosphorelay activation of gene transcription in response to cytokinin.
-Authors: Li, J.X., Zhou, C.M., zhang, P., Wang, J.W.
+The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin.,Zhou CM, Li JX, Zhang TQ, Xu ZG, Ma ML, Zhang P, Wang JW Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2319335121. doi: , 10.1073/pnas.2319335121. Epub 2024 Jan 10. PMID:38198526<ref>PMID:38198526</ref>
-Description: Crystal structure of AtARR1-DBD in complex with a DNA fragment
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Wang, J.W]]
+<div class="pdbe-citations 8xas" style="background-color:#fffaf0;"></div>
-[[Category: Zhang, P]]
+== References ==
-[[Category: Li, J.X]]
+<references/>
-[[Category: Zhou, C.M]]
+__TOC__
+</StructureSection>
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Li JX]]
+[[Category: Wang JW]]
+[[Category: Zhou CM]]
+[[Category: Zhang P]]

8xas

From Proteopedia

Current revision

Crystal structure of AtARR1-DBD in complex with a DNA fragment

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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