6j4r - Revision history

OCA at 10:36, 27 March 2024

OCA — Wed, 27 Mar 2024 10:36:41 GMT

←Older revision		Revision as of 10:36, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6j4r' size='340' side='right'caption='[[6j4r]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6j4r' size='340' side='right'caption='[[6j4r]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j4r]] is a 8 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=6J4R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6J4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j4r]] is a 8 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=6J4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J4R 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]] 2.8Å</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=6j4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4r OCA], [~~http~~://pdbe.org/6j4r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6j4r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6j4r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4r 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=6j4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4r OCA], [https://pdbe.org/6j4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j4r RCSB], [https://www.ebi.ac.uk/pdbsum/6j4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4r 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6j4r" 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: ~~Myb domain dna]]~~	+	[[Category: Sun LF]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 06:55, 31 July 2019

OCA — Wed, 31 Jul 2019 06:55:22 GMT

←Older revision		Revision as of 06:55, 31 July 2019
Line 3:		Line 3:
	<StructureSection load='6j4r' size='340' side='right'caption='[[6j4r]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6j4r' size='340' side='right'caption='[[6j4r]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j4r]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j4r]] is a 8 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=6J4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4R FirstGlance]. <br>
-	</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=6j4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4r OCA], [http://pdbe.org/6j4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4r RCSB], [http://www.ebi.ac.uk/pdbsum/6j4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4r ProSAT]</span></td></tr>	+	</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>
		+	<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=6j4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4r OCA], [http://pdbe.org/6j4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4r RCSB], [http://www.ebi.ac.uk/pdbsum/6j4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Isupov, M N]]		[[Category: Isupov, M N]]

OCA at 06:52, 24 April 2019

OCA — Wed, 24 Apr 2019 06:52:09 GMT

←Older revision		Revision as of 06:52, 24 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6j4r is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structural basis for the target DNA recognition and binding by the MYB domain of phosphate starvation response regulator 1==
		+	<StructureSection load='6j4r' size='340' side='right'caption='[[6j4r]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6j4r]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4R FirstGlance]. <br>
		+	</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=6j4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4r OCA], [http://pdbe.org/6j4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4r RCSB], [http://www.ebi.ac.uk/pdbsum/6j4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4r ProSAT]</span></td></tr>
		+	</table>
		+	== 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>
		+	<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.

-	~~Authors: Jiang~~, M~~.Q.~~, Sun, L~~.F.~~, Isupov, M.N.	+	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>

-	~~Description: Structural basis for~~ the ~~target DNA recognition and binding by the MYB domain~~ of ~~phosphate starvation response regulator 1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Sun~~, ~~L.F~~]]	+	<div class="pdbe-citations 6j4r" style="background-color:#fffaf0;"></div>
-	[[Category: Jiang, M.Q]]	+	== References ==
-	[[Category: ~~Isupov~~, ~~M.N~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Isupov, M N]]
		+	[[Category: Jiang, M Q]]
		+	[[Category: Sun, L F]]
		+	[[Category: Myb domain dna]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription-dna complex]]

OCA at 03:55, 17 April 2019

OCA — Wed, 17 Apr 2019 03:55:05 GMT

←Older revision		Revision as of 03:55, 17 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6j4r is ON HOLD	+	The entry 6j4r is ON HOLD until Paper Publication

	Authors: Jiang, M.Q., Sun, L.F., Isupov, M.N.		Authors: Jiang, M.Q., Sun, L.F., Isupov, M.N.

OCA: Protected "6j4r" [edit=sysop:move=sysop]

OCA — Wed, 16 Jan 2019 10:27:16 GMT

Protected "6j4r" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:27, 16 January 2019

OCA: New page: '''Unreleased structure''' The entry 6j4r is ON HOLD Authors: Jiang, M.Q., Sun, L.F., Isupov, M.N. Description: Structural basis for the target DNA recognition and binding by the MYB d...

OCA — Wed, 16 Jan 2019 10:27:15 GMT

New page: '''Unreleased structure''' The entry 6j4r is ON HOLD Authors: Jiang, M.Q., Sun, L.F., Isupov, M.N. Description: Structural basis for the target DNA recognition and binding by the MYB d...

New page

'''Unreleased structure'''

The entry 6j4r is ON HOLD

Authors: Jiang, M.Q., Sun, L.F., Isupov, M.N.

Description: Structural basis for the target DNA recognition and binding by the MYB domain of phosphate starvation response regulator 1
[[Category: Unreleased Structures]]
[[Category: Sun, L.F]]
[[Category: Jiang, M.Q]]
[[Category: Isupov, M.N]]