6j5b: Difference between revisions

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<StructureSection load='6j5b' size='340' side='right'caption='[[6j5b]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='6j5b' size='340' side='right'caption='[[6j5b]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6j5b]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J5B FirstGlance]. <br>
<table><tr><td colspan='2'>[[6j5b]] is a 12 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=6J5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J5B FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PHR1, At4g28610, T5F17.60 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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]] 2.7&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6j5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j5b OCA], [http://pdbe.org/6j5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j5b RCSB], [http://www.ebi.ac.uk/pdbsum/6j5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j5b 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=6j5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j5b OCA], [https://pdbe.org/6j5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j5b RCSB], [https://www.ebi.ac.uk/pdbsum/6j5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j5b ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/PHR1_ARATH PHR1_ARATH]] Transcription factor involved in phosphate starvation signaling (PubMed:11511543, PubMed:17927693, PubMed:26586833). Binds as a dimer to P1BS, an imperfect palindromic sequence 5'-GNATATNC-3', to promote the expression of inorganic phosphate (Pi) starvation-responsive genes (PubMed:11511543, PubMed:20838596, PubMed:26586833). SPX1 is a competitive inhibitor of this DNA-binding (PubMed:25271326). PHR1 binding to its targets is low Pi-dependent (PubMed:25271326). Regulates the expression of miR399 (PubMed:20838596). Regulates the expression of IPS1 (At3g09922), a non-coding RNA that mimics the target of miR399 to block the cleavage of PHO2 under Pi-deficient conditions (PubMed:17643101). Regulates lipid remodeling and triacylglycerol accumulation during phosphorus starvation (PubMed:25680792). Required for the shoot-specific hypoxic response (PubMed:24753539). Regulates FER1 expression upon phosphate starvation, linking iron and phosphate homeostasis (PubMed:23788639). Contributes to the homeostasis of both sulfate and phosphate in plants under phosphate deficiency (PubMed:21261953). Required for adaptation to high light and retaining functional photosynthesis during phosphate starvation (PubMed:21910737). Involved in the coregulation of Zn and Pi homeostasis (PubMed:24420568).<ref>PMID:11511543</ref> <ref>PMID:17643101</ref> <ref>PMID:17927693</ref> <ref>PMID:20838596</ref> <ref>PMID:21261953</ref> <ref>PMID:21910737</ref> <ref>PMID:23788639</ref> <ref>PMID:24420568</ref> <ref>PMID:24753539</ref> <ref>PMID:25271326</ref> <ref>PMID:25680792</ref> <ref>PMID:26586833</ref> 
[https://www.uniprot.org/uniprot/PHR1_ARATH PHR1_ARATH] Transcription factor involved in phosphate starvation signaling (PubMed:11511543, PubMed:17927693, PubMed:26586833). Binds as a dimer to P1BS, an imperfect palindromic sequence 5'-GNATATNC-3', to promote the expression of inorganic phosphate (Pi) starvation-responsive genes (PubMed:11511543, PubMed:20838596, PubMed:26586833). SPX1 is a competitive inhibitor of this DNA-binding (PubMed:25271326). PHR1 binding to its targets is low Pi-dependent (PubMed:25271326). Regulates the expression of miR399 (PubMed:20838596). Regulates the expression of IPS1 (At3g09922), a non-coding RNA that mimics the target of miR399 to block the cleavage of PHO2 under Pi-deficient conditions (PubMed:17643101). Regulates lipid remodeling and triacylglycerol accumulation during phosphorus starvation (PubMed:25680792). Required for the shoot-specific hypoxic response (PubMed:24753539). Regulates FER1 expression upon phosphate starvation, linking iron and phosphate homeostasis (PubMed:23788639). Contributes to the homeostasis of both sulfate and phosphate in plants under phosphate deficiency (PubMed:21261953). Required for adaptation to high light and retaining functional photosynthesis during phosphate starvation (PubMed:21910737). Involved in the coregulation of Zn and Pi homeostasis (PubMed:24420568).<ref>PMID:11511543</ref> <ref>PMID:17643101</ref> <ref>PMID:17927693</ref> <ref>PMID:20838596</ref> <ref>PMID:21261953</ref> <ref>PMID:21910737</ref> <ref>PMID:23788639</ref> <ref>PMID:24420568</ref> <ref>PMID:24753539</ref> <ref>PMID:25271326</ref> <ref>PMID:25680792</ref> <ref>PMID:26586833</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The phosphate starvation response 1 (PHR1) protein has a central role in mediating the response to phosphate starvation in plants. PHR1 is composed of a number of domains including a MYB domain involved with DNA-binding and a coiled-coil domain proposed to be involved with dimer formation. PHR1 binds to the promoter of phosphate starvation-induced genes to control the levels of phosphate required for nutrition. Previous studies have shown that both the MYB domain and the coiled-coil domain of PHR1 are required for binding the target DNA. Here, we describe the crystal structure of the PHR1 MYB domain and two structures of its complex with the PHR1-binding DNA sequence (P1BS). Structural and isothermal titration calorimetry has been carried out showing that the MYB domain of PHR1 alone is sufficient for target DNA recognition and binding. Two copies of the PHR1 MYB domain bind to the same major groove of the P1BS DNA with few direct interactions between the individual MYB domains. In addition, the PHR1 MYB-P1BS DNA complex structures reveal amino acid residues involved in DNA recognition and binding. Mutagenesis of these residues results in lost or impaired ability of PHR1 MYB to bind to its target DNA. The results presented reveal the structural basis for DNA recognition by the PHR1 MYB domain and demonstrate that two PHR1 MYB domains attach to their P1BS DNA targeting sequence. This article is protected by copyright. All rights reserved.
 
Structural Basis for the Target DNA Recognition and Binding by the MYB Domain of Phosphate Starvation Response 1.,Jiang M, Sun L, Isupov MN, Littlechild JA, Wu X, Wang Q, Wang Q, Yang W, Wu Y FEBS J. 2019 Apr 11. doi: 10.1111/febs.14846. PMID:30974511<ref>PMID:30974511</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6j5b" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arath]]
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Isupov, M N]]
[[Category: Synthetic construct]]
[[Category: Jiang, M Q]]
[[Category: Isupov MN]]
[[Category: Sun, L F]]
[[Category: Jiang MQ]]
[[Category: Wu, Y K]]
[[Category: Sun LF]]
[[Category: Myb domain dna]]
[[Category: Wu YK]]
[[Category: Transcription]]
[[Category: Transcription-dna complex]]

Latest revision as of 13:36, 27 March 2024

Structural basis for the target DNA recognition and binding by the MYB domain of phosphate starvation response regulator 1Structural basis for the target DNA recognition and binding by the MYB domain of phosphate starvation response regulator 1

Structural highlights

6j5b is a 12 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 2.7Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHR1_ARATH Transcription factor involved in phosphate starvation signaling (PubMed:11511543, PubMed:17927693, PubMed:26586833). Binds as a dimer to P1BS, an imperfect palindromic sequence 5'-GNATATNC-3', to promote the expression of inorganic phosphate (Pi) starvation-responsive genes (PubMed:11511543, PubMed:20838596, PubMed:26586833). SPX1 is a competitive inhibitor of this DNA-binding (PubMed:25271326). PHR1 binding to its targets is low Pi-dependent (PubMed:25271326). Regulates the expression of miR399 (PubMed:20838596). Regulates the expression of IPS1 (At3g09922), a non-coding RNA that mimics the target of miR399 to block the cleavage of PHO2 under Pi-deficient conditions (PubMed:17643101). Regulates lipid remodeling and triacylglycerol accumulation during phosphorus starvation (PubMed:25680792). Required for the shoot-specific hypoxic response (PubMed:24753539). Regulates FER1 expression upon phosphate starvation, linking iron and phosphate homeostasis (PubMed:23788639). Contributes to the homeostasis of both sulfate and phosphate in plants under phosphate deficiency (PubMed:21261953). Required for adaptation to high light and retaining functional photosynthesis during phosphate starvation (PubMed:21910737). Involved in the coregulation of Zn and Pi homeostasis (PubMed:24420568).[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]

References

  1. ↑ Rubio V, Linhares F, Solano R, Martin AC, Iglesias J, Leyva A, Paz-Ares J. A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev. 2001 Aug 15;15(16):2122-33. PMID:11511543 doi:http://dx.doi.org/10.1101/gad.204401
  2. ↑ Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, Garcia JA, Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet. 2007 Aug;39(8):1033-7. doi: 10.1038/ng2079. Epub 2007 Jul 22. PMID:17643101 doi:http://dx.doi.org/10.1038/ng2079
  3. ↑ Nilsson L, Muller R, Nielsen TH. Increased expression of the MYB-related transcription factor, PHR1, leads to enhanced phosphate uptake in Arabidopsis thaliana. Plant Cell Environ. 2007 Dec;30(12):1499-512. doi:, 10.1111/j.1365-3040.2007.01734.x. Epub 2007 Oct 9. PMID:17927693 doi:http://dx.doi.org/10.1111/j.1365-3040.2007.01734.x
  4. ↑ Bustos R, Castrillo G, Linhares F, Puga MI, Rubio V, Perez-Perez J, Solano R, Leyva A, Paz-Ares J. A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis. PLoS Genet. 2010 Sep 9;6(9):e1001102. doi: 10.1371/journal.pgen.1001102. PMID:20838596 doi:http://dx.doi.org/10.1371/journal.pgen.1001102
  5. ↑ Rouached H, Secco D, Arpat B, Poirier Y. The transcription factor PHR1 plays a key role in the regulation of sulfate shoot-to-root flux upon phosphate starvation in Arabidopsis. BMC Plant Biol. 2011 Jan 24;11:19. doi: 10.1186/1471-2229-11-19. PMID:21261953 doi:http://dx.doi.org/10.1186/1471-2229-11-19
  6. ↑ Nilsson L, Lundmark M, Jensen PE, Nielsen TH. The Arabidopsis transcription factor PHR1 is essential for adaptation to high light and retaining functional photosynthesis during phosphate starvation. Physiol Plant. 2012 Jan;144(1):35-47. doi: 10.1111/j.1399-3054.2011.01520.x. Epub, 2011 Oct 19. PMID:21910737 doi:http://dx.doi.org/10.1111/j.1399-3054.2011.01520.x
  7. ↑ Bournier M, Tissot N, Mari S, Boucherez J, Lacombe E, Briat JF, Gaymard F. Arabidopsis ferritin 1 (AtFer1) gene regulation by the phosphate starvation response 1 (AtPHR1) transcription factor reveals a direct molecular link between iron and phosphate homeostasis. J Biol Chem. 2013 Aug 2;288(31):22670-80. doi: 10.1074/jbc.M113.482281. Epub 2013, Jun 20. PMID:23788639 doi:http://dx.doi.org/10.1074/jbc.M113.482281
  8. ↑ Khan GA, Bouraine S, Wege S, Li Y, de Carbonnel M, Berthomieu P, Poirier Y, Rouached H. Coordination between zinc and phosphate homeostasis involves the transcription factor PHR1, the phosphate exporter PHO1, and its homologue PHO1;H3 in Arabidopsis. J Exp Bot. 2014 Mar;65(3):871-84. doi: 10.1093/jxb/ert444. Epub 2014 Jan 13. PMID:24420568 doi:http://dx.doi.org/10.1093/jxb/ert444
  9. ↑ Klecker M, Gasch P, Peisker H, Dormann P, Schlicke H, Grimm B, Mustroph A. A Shoot-Specific Hypoxic Response of Arabidopsis Sheds Light on the Role of the Phosphate-Responsive Transcription Factor PHOSPHATE STARVATION RESPONSE1. Plant Physiol. 2014 Jun;165(2):774-790. doi: 10.1104/pp.114.237990. Epub 2014 Apr, 21. PMID:24753539 doi:http://dx.doi.org/10.1104/pp.114.237990
  10. ↑ Puga MI, Mateos I, Charukesi R, Wang Z, Franco-Zorrilla JM, de Lorenzo L, Irigoyen ML, Masiero S, Bustos R, Rodriguez J, Leyva A, Rubio V, Sommer H, Paz-Ares J. SPX1 is a phosphate-dependent inhibitor of Phosphate Starvation Response 1 in Arabidopsis. Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14947-52. doi:, 10.1073/pnas.1404654111. Epub 2014 Sep 30. PMID:25271326 doi:http://dx.doi.org/10.1073/pnas.1404654111
  11. ↑ Pant BD, Burgos A, Pant P, Cuadros-Inostroza A, Willmitzer L, Scheible WR. The transcription factor PHR1 regulates lipid remodeling and triacylglycerol accumulation in Arabidopsis thaliana during phosphorus starvation. J Exp Bot. 2015 Apr;66(7):1907-18. doi: 10.1093/jxb/eru535. Epub 2015 Feb 13. PMID:25680792 doi:http://dx.doi.org/10.1093/jxb/eru535
  12. ↑ Sun L, Song L, Zhang Y, Zheng Z, Liu D. Arabidopsis PHL2 and PHR1 Act Redundantly as the Key Components of the Central Regulatory System Controlling Transcriptional Responses to Phosphate Starvation. Plant Physiol. 2016 Jan;170(1):499-514. doi: 10.1104/pp.15.01336. Epub 2015 Nov, 19. PMID:26586833 doi:http://dx.doi.org/10.1104/pp.15.01336

6j5b, resolution 2.70Å

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