6kks

From Proteopedia

(Difference between revisions)

Current revision

Structural insights into target DNA recognition by R2R3-type MYB transcription factor

Structural highlights

6kks is a 3 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.15Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

WER_ARATH Transcription activator, when associated with BHLH2/EGL3/MYC146 or BHLH12/MYC1. Involved in epidermal cell fate specification in roots and hypocotyl. Together with GL3 or BHLH2, promotes the formation of non-hair developing cells (atrichoblasts) et the N position in root epidermis. Regulates stomata spatial distribution in hypocotyls. Binds to the WER-binding sites (WBS) promoter regions and activates the transcription of target genes such as GL2 and of CPC.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

As the largest group of MYB family transcription factors, R2R3-MYB proteins play essential roles during plant growth and development. However, the structural basis underlying how R2R3-MYBs recognize the target DNA remains elusive. Here, we report the crystal structure of Arabidopsis WEREWOLF (WER), an R2R3-MYB protein, in complex with its target DNA. Structural analysis showed that the third alpha-helices in both the R2 and R3 repeats of WER fit in the major groove of the DNA, specifically recognizing the DNA motif 5'-AACNGC-3'. In combination with mutagenesis, in vitro binding and in vivo luciferase assays, we showed that K55, N106, K109 and N110 are critical for the function of WER. Although L59 of WER is not involved in DNA binding in the structure, ITC analysis suggested that L59 plays an important role in sensing DNA methylation at the fifth position of cytosine (5mC). Like 5mC, methylation at the sixth position of adenine (6mA) in the AAC element also inhibits the interaction between WER and its target DNA. Our study not only unravels the molecular basis of how WER recognizes its target DNA, but also suggests that 5mC and 6mA modifications may block the interaction between R2R3-MYB transcription factors and their target genes.

Structural insights into target DNA recognition by R2R3-MYB transcription factors.,Wang B, Luo Q, Li Y, Yin L, Zhou N, Li X, Gan J, Dong A Nucleic Acids Res. 2019 Nov 16. pii: 5626523. doi: 10.1093/nar/gkz1081. PMID:31733060^[7]

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

References

↑ Lee MM, Schiefelbein J. WEREWOLF, a MYB-related protein in Arabidopsis, is a position-dependent regulator of epidermal cell patterning. Cell. 1999 Nov 24;99(5):473-83. doi: 10.1016/s0092-8674(00)81536-6. PMID:10589676 doi:http://dx.doi.org/10.1016/s0092-8674(00)81536-6
↑ Lin Y, Schiefelbein J. Embryonic control of epidermal cell patterning in the root and hypocotyl of Arabidopsis. Development. 2001 Oct;128(19):3697-705. PMID:11585796
↑ Bernhardt C, Lee MM, Gonzalez A, Zhang F, Lloyd A, Schiefelbein J. The bHLH genes GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3) specify epidermal cell fate in the Arabidopsis root. Development. 2003 Dec;130(26):6431-9. Epub 2003 Nov 19. PMID:14627722 doi:http://dx.doi.org/10.1242/dev.00880
↑ Zimmermann IM, Heim MA, Weisshaar B, Uhrig JF. Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. Plant J. 2004 Oct;40(1):22-34. doi: 10.1111/j.1365-313X.2004.02183.x. PMID:15361138 doi:http://dx.doi.org/10.1111/j.1365-313X.2004.02183.x
↑ Koshino-Kimura Y, Wada T, Tachibana T, Tsugeki R, Ishiguro S, Okada K. Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis. Plant Cell Physiol. 2005 Jun;46(6):817-26. Epub 2005 Mar 28. PMID:15795220 doi:http://dx.doi.org/pci096
↑ Ryu KH, Kang YH, Park YH, Hwang I, Schiefelbein J, Lee MM. The WEREWOLF MYB protein directly regulates CAPRICE transcription during cell fate specification in the Arabidopsis root epidermis. Development. 2005 Nov;132(21):4765-75. Epub 2005 Oct 5. PMID:16207757 doi:http://dx.doi.org/dev.02055
↑ Wang B, Luo Q, Li Y, Yin L, Zhou N, Li X, Gan J, Dong A. Structural insights into target DNA recognition by R2R3-MYB transcription factors. Nucleic Acids Res. 2019 Nov 16. pii: 5626523. doi: 10.1093/nar/gkz1081. PMID:31733060 doi:http://dx.doi.org/10.1093/nar/gkz1081

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/6kks"

Categories: Arabidopsis thaliana | Large Structures | Luo Q | Wang B

@@ Line 3: / Line 3: @@
 <StructureSection load='6kks' size='340' side='right'caption='[[6kks]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6kks]] is a 3 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=6KKS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KKS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6kks]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KKS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 2.15&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">WER ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6kks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kks OCA], [http://pdbe.org/6kks PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kks RCSB], [http://www.ebi.ac.uk/pdbsum/6kks PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kks 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=6kks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kks OCA], [https://pdbe.org/6kks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kks RCSB], [https://www.ebi.ac.uk/pdbsum/6kks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kks ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/WER_ARATH WER_ARATH]] Transcription activator, when associated with BHLH2/EGL3/MYC146 or BHLH12/MYC1. Involved in epidermal cell fate specification in roots and hypocotyl. Together with GL3 or BHLH2, promotes the formation of non-hair developing cells (atrichoblasts) et the N position in root epidermis. Regulates stomata spatial distribution in hypocotyls. Binds to the WER-binding sites (WBS) promoter regions and activates the transcription of target genes such as GL2 and of CPC.<ref>PMID:10589676</ref> <ref>PMID:11585796</ref> <ref>PMID:14627722</ref> <ref>PMID:15361138</ref> <ref>PMID:15795220</ref> <ref>PMID:16207757</ref>
+[https://www.uniprot.org/uniprot/WER_ARATH WER_ARATH] Transcription activator, when associated with BHLH2/EGL3/MYC146 or BHLH12/MYC1. Involved in epidermal cell fate specification in roots and hypocotyl. Together with GL3 or BHLH2, promotes the formation of non-hair developing cells (atrichoblasts) et the N position in root epidermis. Regulates stomata spatial distribution in hypocotyls. Binds to the WER-binding sites (WBS) promoter regions and activates the transcription of target genes such as GL2 and of CPC.<ref>PMID:10589676</ref> <ref>PMID:11585796</ref> <ref>PMID:14627722</ref> <ref>PMID:15361138</ref> <ref>PMID:15795220</ref> <ref>PMID:16207757</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Luo, Q]]
+[[Category: Luo Q]]
-[[Category: Wang, B]]
+[[Category: Wang B]]
-[[Category: Dna binding protein-dna complex]]
-[[Category: Transcription factor]]

6kks

From Proteopedia

Current revision

Structural insights into target DNA recognition by R2R3-type MYB transcription factor

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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