7xp3 | pdb_00007xp3

DNA complex form of ORESARA1(ANAC092) NAC Domain

Structural highlights

7xp3 is a 7 chain structure with sequence from Arabidopsis thaliana and DNA molecule. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.25Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

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.

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^[10]

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

References

↑ Woo HR, Kim JH, Nam HG, Lim PO. The delayed leaf senescence mutants of Arabidopsis, ore1, ore3, and ore9 are tolerant to oxidative stress. Plant Cell Physiol. 2004 Jul;45(7):923-32. PMID:15295076 doi:10.1093/pcp/pch110
↑ He XJ, Mu RL, Cao WH, Zhang ZG, Zhang JS, Chen SY. AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J. 2005 Dec;44(6):903-16. PMID:16359384 doi:10.1111/j.1365-313X.2005.02575.x
↑ Kim JH, Woo HR, Kim J, Lim PO, Lee IC, Choi SH, Hwang D, Nam HG. Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science. 2009 Feb 20;323(5917):1053-7. PMID:19229035 doi:10.1126/science.1166386
↑ Carviel JL, Al-Daoud F, Neumann M, Mohammad A, Provart NJ, Moeder W, Yoshioka K, Cameron RK. Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana. Mol Plant Pathol. 2009 Sep;10(5):621-34. PMID:19694953 doi:10.1111/j.1364-3703.2009.00557.x
↑ Balazadeh S, Siddiqui H, Allu AD, Matallana-Ramirez LP, Caldana C, Mehrnia M, Zanor MI, Köhler B, Mueller-Roeber B. A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J. 2010 Apr;62(2):250-64. PMID:20113437 doi:10.1111/j.1365-313X.2010.04151.x
↑ Balazadeh S, Kwasniewski M, Caldana C, Mehrnia M, Zanor MI, Xue GP, Mueller-Roeber B. ORS1, an H₂O₂-responsive NAC transcription factor, controls senescence in Arabidopsis thaliana. Mol Plant. 2011 Mar;4(2):346-60. PMID:21303842 doi:10.1093/mp/ssq080
↑ Matallana-Ramirez LP, Rauf M, Farage-Barhom S, Dortay H, Xue GP, Dröge-Laser W, Lers A, Balazadeh S, Mueller-Roeber B. NAC transcription factor ORE1 and senescence-induced BIFUNCTIONAL NUCLEASE1 (BFN1) constitute a regulatory cascade in Arabidopsis. Mol Plant. 2013 Sep;6(5):1438-52. PMID:23340744 doi:10.1093/mp/sst012
↑ Rauf M, Arif M, Dortay H, Matallana-Ramírez LP, Waters MT, Gil Nam H, Lim PO, Mueller-Roeber B, Balazadeh S. ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription. EMBO Rep. 2013 Apr;14(4):382-8. PMID:23459204 doi:10.1038/embor.2013.24
↑ Oh SA, Park JH, Lee GI, Paek KH, Park SK, Nam HG. Identification of three genetic loci controlling leaf senescence in Arabidopsis thaliana. Plant J. 1997 Sep;12(3):527-35. PMID:9351240 doi:10.1046/j.1365-313x.1997.00527.x
↑ Chun I, Kim HJ, Hong S, Kim YG, Kim MS. Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence. Plant Commun. 2023 May 8;4(3):100510. PMID:36564947 doi:10.1016/j.xplc.2022.100510

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[1] Woo HR, Kim JH, Nam HG, Lim PO. The delayed leaf senescence mutants of Arabidopsis, ore1, ore3, and ore9 are tolerant to oxidative stress. Plant Cell Physiol. 2004 Jul;45(7):923-32. PMID:15295076 doi:10.1093/pcp/pch110

[2] He XJ, Mu RL, Cao WH, Zhang ZG, Zhang JS, Chen SY. AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J. 2005 Dec;44(6):903-16. PMID:16359384 doi:10.1111/j.1365-313X.2005.02575.x

[3] Kim JH, Woo HR, Kim J, Lim PO, Lee IC, Choi SH, Hwang D, Nam HG. Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science. 2009 Feb 20;323(5917):1053-7. PMID:19229035 doi:10.1126/science.1166386

[4] Carviel JL, Al-Daoud F, Neumann M, Mohammad A, Provart NJ, Moeder W, Yoshioka K, Cameron RK. Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana. Mol Plant Pathol. 2009 Sep;10(5):621-34. PMID:19694953 doi:10.1111/j.1364-3703.2009.00557.x

[5] Balazadeh S, Siddiqui H, Allu AD, Matallana-Ramirez LP, Caldana C, Mehrnia M, Zanor MI, Köhler B, Mueller-Roeber B. A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J. 2010 Apr;62(2):250-64. PMID:20113437 doi:10.1111/j.1365-313X.2010.04151.x

[6] Balazadeh S, Kwasniewski M, Caldana C, Mehrnia M, Zanor MI, Xue GP, Mueller-Roeber B. ORS1, an H₂O₂-responsive NAC transcription factor, controls senescence in Arabidopsis thaliana. Mol Plant. 2011 Mar;4(2):346-60. PMID:21303842 doi:10.1093/mp/ssq080

[7] Matallana-Ramirez LP, Rauf M, Farage-Barhom S, Dortay H, Xue GP, Dröge-Laser W, Lers A, Balazadeh S, Mueller-Roeber B. NAC transcription factor ORE1 and senescence-induced BIFUNCTIONAL NUCLEASE1 (BFN1) constitute a regulatory cascade in Arabidopsis. Mol Plant. 2013 Sep;6(5):1438-52. PMID:23340744 doi:10.1093/mp/sst012

[8] Rauf M, Arif M, Dortay H, Matallana-Ramírez LP, Waters MT, Gil Nam H, Lim PO, Mueller-Roeber B, Balazadeh S. ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription. EMBO Rep. 2013 Apr;14(4):382-8. PMID:23459204 doi:10.1038/embor.2013.24

[9] Oh SA, Park JH, Lee GI, Paek KH, Park SK, Nam HG. Identification of three genetic loci controlling leaf senescence in Arabidopsis thaliana. Plant J. 1997 Sep;12(3):527-35. PMID:9351240 doi:10.1046/j.1365-313x.1997.00527.x

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

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7xp3 | pdb_00007xp3

DNA complex form of ORESARA1(ANAC092) NAC Domain

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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