5gnj

From Proteopedia

(Difference between revisions)

Revision as of 11:37, 2 August 2023

Structure of a transcription factor and DNA complex

Structural highlights

5gnj is a 16 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

MYC2_ARATH Transcriptional activator. Common transcription factor of light, abscisic acid (ABA), and jasmonic acid (JA) signaling pathways. With MYC3 and MYC4, controls additively subsets of JA-dependent responses. In cooperation with MYB2 is involved in the regulation of ABA-inducible genes under drought stress conditions. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the MYC recognition site (5'-CACATG-3'), and to the G-box (5'-CACNTG-3') and Z-box (5'-ATACGTGT-3') of promoters. Binds directly to the promoters of the transcription factors PLETHORA1 (PLT1) and PLT2 and represses their expression. Negative regulator of blue light-mediated photomorphogenic growth and blue- and far-red-light regulated gene expression. Activates multiple TIFY/JAZ promoters. Positive regulator of lateral root formation. Regulates sesquiterpene biosynthesis. Subjected to proteasome-dependent proteolysis. The presence of the destruction element (DE) involved in turnover is required for the function to regulate gene transcription.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

Publication Abstract from PubMed

Jasmonates (JAs) are essential plant hormones that play important roles in the regulation of plant growth and the response to environmental stress. In the JA signaling pathway, the core transcription factors are a class of basic helix-loop-helix (bHLH) proteins, including MYC2, MYC3, and MYC4, that have different regulatory capacities. Here, we report the 2.7 A crystal structure of the MYC2 bHLH domain complexed with G-box DNA, showing a cis-tetrameric structure. Biochemical assays confirmed that full-length MYC2 forms a stable homo-tetramer both in solution and in DNA-bound states, whereas MYC3 forms only a homodimer. Isothermal titration calorimetry (ITC) assays demonstrated that tetramerization enhanced DNA binding affinity, and fluorescence resonance energy transfer (FRET) assay indicated DNA looping potential of tetrameric MYC2. Luciferase assay further confirmed the importance of tetramerization in transcriptional regulation. Our studies provide a mechanistic explanation for the regulatory differences of MYC transcription factors.

Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA.,Lian TF, Xu YP, Li LF, Su XD Cell Rep. 2017 May 16;19(7):1334-1342. doi: 10.1016/j.celrep.2017.04.057. PMID:28514654^[12]

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

References

↑ Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell. 2003 Jan;15(1):63-78. PMID:12509522
↑ Lorenzo O, Chico JM, Sanchez-Serrano JJ, Solano R. JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis. Plant Cell. 2004 Jul;16(7):1938-50. Epub 2004 Jun 18. PMID:15208388 doi:http://dx.doi.org/10.1105/tpc.022319
↑ Yadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S. A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth. Plant Cell. 2005 Jul;17(7):1953-66. Epub 2005 May 27. PMID:15923349 doi:http://dx.doi.org/tpc.105.032060
↑ Niu Y, Figueroa P, Browse J. Characterization of JAZ-interacting bHLH transcription factors that regulate jasmonate responses in Arabidopsis. J Exp Bot. 2011 Mar;62(6):2143-54. doi: 10.1093/jxb/erq408. Epub 2011 Feb 14. PMID:21321051 doi:http://dx.doi.org/10.1093/jxb/erq408
↑ Fernandez-Calvo P, Chini A, Fernandez-Barbero G, Chico JM, Gimenez-Ibanez S, Geerinck J, Eeckhout D, Schweizer F, Godoy M, Franco-Zorrilla JM, Pauwels L, Witters E, Puga MI, Paz-Ares J, Goossens A, Reymond P, De Jaeger G, Solano R. The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses. Plant Cell. 2011 Feb;23(2):701-15. doi: 10.1105/tpc.110.080788. Epub 2011 Feb 18. PMID:21335373 doi:http://dx.doi.org/10.1105/tpc.110.080788
↑ Chen Q, Sun J, Zhai Q, Zhou W, Qi L, Xu L, Wang B, Chen R, Jiang H, Qi J, Li X, Palme K, Li C. The basic helix-loop-helix transcription factor MYC2 directly represses PLETHORA expression during jasmonate-mediated modulation of the root stem cell niche in Arabidopsis. Plant Cell. 2011 Sep;23(9):3335-52. doi: 10.1105/tpc.111.089870. Epub 2011 Sep, 27. PMID:21954460 doi:http://dx.doi.org/10.1105/tpc.111.089870
↑ Hong GJ, Xue XY, Mao YB, Wang LJ, Chen XY. Arabidopsis MYC2 interacts with DELLA proteins in regulating sesquiterpene synthase gene expression. Plant Cell. 2012 Jun;24(6):2635-48. doi: 10.1105/tpc.112.098749. Epub 2012 Jun 5. PMID:22669881 doi:http://dx.doi.org/10.1105/tpc.112.098749
↑ Kazan K, Manners JM. MYC2: the master in action. Mol Plant. 2013 May;6(3):686-703. doi: 10.1093/mp/sss128. Epub 2012 Nov 9. PMID:23142764 doi:http://dx.doi.org/10.1093/mp/sss128
↑ Zhai Q, Yan L, Tan D, Chen R, Sun J, Gao L, Dong MQ, Wang Y, Li C. Phosphorylation-coupled proteolysis of the transcription factor MYC2 is important for jasmonate-signaled plant immunity. PLoS Genet. 2013 Apr;9(4):e1003422. doi: 10.1371/journal.pgen.1003422. Epub 2013 , Apr 4. PMID:23593022 doi:http://dx.doi.org/10.1371/journal.pgen.1003422
↑ Schweizer F, Fernandez-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker JR, Solano R, Reymond P. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. Plant Cell. 2013 Aug;25(8):3117-32. doi: 10.1105/tpc.113.115139. Epub 2013 Aug, 13. PMID:23943862 doi:http://dx.doi.org/10.1105/tpc.113.115139
↑ Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K. Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell. 1997 Oct;9(10):1859-68. PMID:9368419 doi:http://dx.doi.org/10.1105/tpc.9.10.1859
↑ Lian TF, Xu YP, Li LF, Su XD. Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA. Cell Rep. 2017 May 16;19(7):1334-1342. doi: 10.1016/j.celrep.2017.04.057. PMID:28514654 doi:http://dx.doi.org/10.1016/j.celrep.2017.04.057

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/5gnj"

@@ Line 1: / Line 1: @@
 ==Structure of a transcription factor and DNA complex==
-<StructureSection load='5gnj' size='340' side='right' caption='[[5gnj]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='5gnj' size='340' side='right'caption='[[5gnj]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gnj]] is a 16 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=5GNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GNJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gnj]] is a 16 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=5GNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GNJ FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MYC2 ([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=5gnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gnj OCA], [http://pdbe.org/5gnj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gnj RCSB], [http://www.ebi.ac.uk/pdbsum/5gnj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gnj 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=5gnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gnj OCA], [https://pdbe.org/5gnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gnj RCSB], [https://www.ebi.ac.uk/pdbsum/5gnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gnj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MYC2_ARATH MYC2_ARATH]] Transcriptional activator. Common transcription factor of light, abscisic acid (ABA), and jasmonic acid (JA) signaling pathways. With MYC3 and MYC4, controls additively subsets of JA-dependent responses. In cooperation with MYB2 is involved in the regulation of ABA-inducible genes under drought stress conditions. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the MYC recognition site (5'-CACATG-3'), and to the G-box (5'-CACNTG-3') and Z-box (5'-ATACGTGT-3') of promoters. Binds directly to the promoters of the transcription factors PLETHORA1 (PLT1) and PLT2 and represses their expression. Negative regulator of blue light-mediated photomorphogenic growth and blue- and far-red-light regulated gene expression. Activates multiple TIFY/JAZ promoters. Positive regulator of lateral root formation. Regulates sesquiterpene biosynthesis. Subjected to proteasome-dependent proteolysis. The presence of the destruction element (DE) involved in turnover is required for the function to regulate gene transcription.<ref>PMID:12509522</ref> <ref>PMID:15208388</ref> <ref>PMID:15923349</ref> <ref>PMID:21321051</ref> <ref>PMID:21335373</ref> <ref>PMID:21954460</ref> <ref>PMID:22669881</ref> <ref>PMID:23142764</ref> <ref>PMID:23593022</ref> <ref>PMID:23943862</ref> <ref>PMID:9368419</ref>
+[https://www.uniprot.org/uniprot/MYC2_ARATH MYC2_ARATH] Transcriptional activator. Common transcription factor of light, abscisic acid (ABA), and jasmonic acid (JA) signaling pathways. With MYC3 and MYC4, controls additively subsets of JA-dependent responses. In cooperation with MYB2 is involved in the regulation of ABA-inducible genes under drought stress conditions. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the MYC recognition site (5'-CACATG-3'), and to the G-box (5'-CACNTG-3') and Z-box (5'-ATACGTGT-3') of promoters. Binds directly to the promoters of the transcription factors PLETHORA1 (PLT1) and PLT2 and represses their expression. Negative regulator of blue light-mediated photomorphogenic growth and blue- and far-red-light regulated gene expression. Activates multiple TIFY/JAZ promoters. Positive regulator of lateral root formation. Regulates sesquiterpene biosynthesis. Subjected to proteasome-dependent proteolysis. The presence of the destruction element (DE) involved in turnover is required for the function to regulate gene transcription.<ref>PMID:12509522</ref> <ref>PMID:15208388</ref> <ref>PMID:15923349</ref> <ref>PMID:21321051</ref> <ref>PMID:21335373</ref> <ref>PMID:21954460</ref> <ref>PMID:22669881</ref> <ref>PMID:23142764</ref> <ref>PMID:23593022</ref> <ref>PMID:23943862</ref> <ref>PMID:9368419</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Lian, T]]
+[[Category: Large Structures]]
-[[Category: Su, X]]
+[[Category: Synthetic construct]]
-[[Category: Xu, Y]]
+[[Category: Lian T]]
-[[Category: Complex]]
+[[Category: Su X]]
-[[Category: Dna]]
+[[Category: Xu Y]]
-[[Category: Dna binding protein-dna complex]]
-[[Category: Transcription factor]]

5gnj

From Proteopedia

Revision as of 11:37, 2 August 2023

Structure of a transcription factor and DNA complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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