7xp3 - Revision history

OCA at 19:46, 29 May 2024

2024-05-29T19:46:14Z

← Older revision		Revision as of 19:46, 29 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7xp3]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/DNA_molecule DNA molecule]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XP3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7xp3]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/DNA_molecule DNA molecule]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XP3 FirstGlance]. <br>
	</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=7xp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xp3 OCA], [https://pdbe.org/7xp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7xp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xp3 ProSAT]</span></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]] 3.25Å</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=7xp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xp3 OCA], [https://pdbe.org/7xp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7xp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xp3 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/NAC92_ARATH NAC92_ARATH] Transcription activator that binds to DNA in promoters of target genes on a specific bipartite motif 5'-[ACG][CA]GT[AG](5-6n)[CT]AC[AG]-3' (PubMed:23340744). Promotes lateral root development (PubMed:16359384). Triggers the expression of senescence-associated genes during age-, salt- and dark-induced senescence through a regulatory network that may involve cross-talk with salt- and H(2)O(2)-dependent signaling pathways (PubMed:15295076, PubMed:20113437, PubMed:21303842, PubMed:9351240). Also regulates genes during seed germination (PubMed:20113437). Positively regulates aging-induced cell death (PubMed:19229035). Involved in age-related resistance (ARR) against Pseudomonas syringae pv. tomato and Hyaloperonospora arabidopsidis (PubMed:19694953). Antagonizes GLK1 and GLK2 transcriptional activity, shifting the balance from chloroplast maintenance towards deterioration during leaf senescence (PubMed:23459204). Promotes the expression of senescence-associated genes, including ENDO1/BFN1, SWEET15/SAG29 and SINA1/At3g13672, during senescence onset (PubMed:23340744).<ref>PMID:15295076</ref> <ref>PMID:16359384</ref> <ref>PMID:19229035</ref> <ref>PMID:19694953</ref> <ref>PMID:20113437</ref> <ref>PMID:21303842</ref> <ref>PMID:23340744</ref> <ref>PMID:23459204</ref> <ref>PMID:9351240</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Plants use sophisticated mechanisms of gene expression to control senescence in response to environmental stress or aging. ORE1 (Arabidopsis thaliana NAC092) is a master regulator of senescence that belongs to the plant-specific NAC transcription factor protein family. ORE1 has been reported to bind to multiple DNA targets to orchestrate leaf senescence, yet the mechanistic basis for recognition of the cognate gene sequence remains unclear. Here, we report the crystal structure of the ORE1-NAC domain alone and its DNA-binding form. The structure of DNA-bound ORE1-NAC revealed the molecular basis for nucleobase recognition and phosphate backbone interactions. We show that local versatility in the DNA-binding site, in combination with domain flexibility of the ORE-NAC homodimer, is crucial for the maintenance of binding to intrinsically flexible DNA. Our results provide a platform for understanding other plant-specific NAC protein-DNA interactions as well as insight into the structural basis of NAC regulators in plants of agronomic and scientific importance.		Plants use sophisticated mechanisms of gene expression to control senescence in response to environmental stress or aging. ORE1 (Arabidopsis thaliana NAC092) is a master regulator of senescence that belongs to the plant-specific NAC transcription factor protein family. ORE1 has been reported to bind to multiple DNA targets to orchestrate leaf senescence, yet the mechanistic basis for recognition of the cognate gene sequence remains unclear. Here, we report the crystal structure of the ORE1-NAC domain alone and its DNA-binding form. The structure of DNA-bound ORE1-NAC revealed the molecular basis for nucleobase recognition and phosphate backbone interactions. We show that local versatility in the DNA-binding site, in combination with domain flexibility of the ORE-NAC homodimer, is crucial for the maintenance of binding to intrinsically flexible DNA. Our results provide a platform for understanding other plant-specific NAC protein-DNA interactions as well as insight into the structural basis of NAC regulators in plants of agronomic and scientific importance.

	Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence.,Chun I, Kim HJ, Hong S, Kim YG, Kim MS Plant Commun. ~~2022 Dec 23~~:100510. doi: 10.1016/j.xplc.2022.100510. PMID:36564947<ref>PMID:36564947</ref>		Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence.,Chun I, Kim HJ, Hong S, Kim YG, Kim MS Plant Commun. 2023 May 8;4(3):100510. doi: 10.1016/j.xplc.2022.100510. Epub 2022 , Dec 23. PMID:36564947<ref>PMID:36564947</ref>

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

OCA at 06:42, 29 March 2023

2023-03-29T06:42:27Z

← Older revision		Revision as of 06:42, 29 March 2023
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7xp3 is ~~ON HOLD until Paper~~ Publication		==DNA complex form of ORESARA1(ANAC092) NAC Domain==
			<StructureSection load='7xp3' size='340' side='right'caption='[[7xp3]], [[Resolution\|resolution]] 3.25Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[7xp3]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/DNA_molecule DNA molecule]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XP3 FirstGlance]. <br>
			</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=7xp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xp3 OCA], [https://pdbe.org/7xp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7xp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xp3 ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Plants use sophisticated mechanisms of gene expression to control senescence in response to environmental stress or aging. ORE1 (Arabidopsis thaliana NAC092) is a master regulator of senescence that belongs to the plant-specific NAC transcription factor protein family. ORE1 has been reported to bind to multiple DNA targets to orchestrate leaf senescence, yet the mechanistic basis for recognition of the cognate gene sequence remains unclear. Here, we report the crystal structure of the ORE1-NAC domain alone and its DNA-binding form. The structure of DNA-bound ORE1-NAC revealed the molecular basis for nucleobase recognition and phosphate backbone interactions. We show that local versatility in the DNA-binding site, in combination with domain flexibility of the ORE-NAC homodimer, is crucial for the maintenance of binding to intrinsically flexible DNA. Our results provide a platform for understanding other plant-specific NAC protein-DNA interactions as well as insight into the structural basis of NAC regulators in plants of agronomic and scientific importance.

	~~Authors:~~ Chun, I.S., Kim, M.S.		Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence.,Chun I, Kim HJ, Hong S, Kim YG, Kim MS Plant Commun. 2022 Dec 23:100510. doi: 10.1016/j.xplc.2022.100510. PMID:36564947<ref>PMID:36564947</ref>

	~~Description~~: DNA ~~complex form of ORESARA1(ANAC092) NAC Domain~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: ~~Kim, M.S~~]]		<div class="pdbe-citations 7xp3" style="background-color:#fffaf0;"></div>
	[[Category: ~~Chun, I.S~~]]		== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Arabidopsis thaliana]]
			[[Category: DNA molecule]]
			[[Category: Large Structures]]
			[[Category: Chun IS]]
			[[Category: Kim MS]]

OCA at 07:00, 22 June 2022

2022-06-22T07:00:27Z

← Older revision		Revision as of 07:00, 22 June 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7xp3 is ON HOLD		The entry 7xp3 is ON HOLD until Paper Publication

	Authors: Chun, I.S., Kim, M.S.		Authors: Chun, I.S., Kim, M.S.

OCA: Protected "7xp3" [edit=sysop:move=sysop]

2022-05-12T04:57:56Z

Protected "7xp3" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:57, 12 May 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7xp3 is ON HOLD Authors: Chun, I.S., Kim, M.S. Description: DNA complex form of ORESARA1(ANAC092) NAC Domain Category: Unreleased Structures [[...

2022-05-12T04:57:55Z

New page: '''Unreleased structure''' The entry 7xp3 is ON HOLD Authors: Chun, I.S., Kim, M.S. Description: DNA complex form of ORESARA1(ANAC092) NAC Domain Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 7xp3 is ON HOLD

Authors: Chun, I.S., Kim, M.S.

Description: DNA complex form of ORESARA1(ANAC092) NAC Domain
[[Category: Unreleased Structures]]
[[Category: Kim, M.S]]
[[Category: Chun, I.S]]