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==Crystal structure of the DNA binding domain of A. thailana auxin response factor 1==
==Crystal structure of the DNA binding domain of A. thailana auxin response factor 1==
<StructureSection load='4ldv' size='340' side='right' caption='[[4ldv]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
<StructureSection load='4ldv' size='340' side='right'caption='[[4ldv]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ldv]] is a 1 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=4LDV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LDV FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ldv]] is a 1 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=4LDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LDV FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 1.45&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ldw|4ldw]], [[4ldx|4ldx]], [[4ldy|4ldy]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARF1, At1g59750, F23H11.7 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=4ldv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ldv OCA], [https://pdbe.org/4ldv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ldv RCSB], [https://www.ebi.ac.uk/pdbsum/4ldv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ldv ProSAT]</span></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=4ldv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ldv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ldv RCSB], [http://www.ebi.ac.uk/pdbsum/4ldv PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ARFA_ARATH ARFA_ARATH]] Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Seems to act as transcriptional repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Acts as repressor of IAA2, IAA3 and IAA7.<ref>PMID:12036261</ref> <ref>PMID:16176952</ref> 
[https://www.uniprot.org/uniprot/ARFA_ARATH ARFA_ARATH] Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Seems to act as transcriptional repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Acts as repressor of IAA2, IAA3 and IAA7.<ref>PMID:12036261</ref> <ref>PMID:16176952</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.
 
Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors.,Boer DR, Freire-Rios A, van den Berg WA, Saaki T, Manfield IW, Kepinski S, Lopez-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D, Coll M Cell. 2014 Jan 30;156(3):577-89. doi: 10.1016/j.cell.2013.12.027. PMID:24485461<ref>PMID:24485461</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arath]]
[[Category: Arabidopsis thaliana]]
[[Category: Berg, W M.A van den]]
[[Category: Large Structures]]
[[Category: Coll, M]]
[[Category: Coll M]]
[[Category: Freire-Rios, A]]
[[Category: Freire-Rios A]]
[[Category: Weijers, D]]
[[Category: Weijers D]]
[[Category: Boer, D R]]
[[Category: Boer DR]]
[[Category: Dna binding]]
[[Category: Van den Berg WMA]]
[[Category: Nucleus]]
[[Category: Transcription]]
[[Category: Transcription factor]]

Latest revision as of 15:19, 1 March 2024

Crystal structure of the DNA binding domain of A. thailana auxin response factor 1Crystal structure of the DNA binding domain of A. thailana auxin response factor 1

Structural highlights

4ldv is a 1 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 1.45Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARFA_ARATH Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Seems to act as transcriptional repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Acts as repressor of IAA2, IAA3 and IAA7.[1] [2]

References

  1. ↑ Hagen G, Guilfoyle T. Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol. 2002 Jun-Jul;49(3-4):373-85. PMID:12036261
  2. ↑ Ellis CM, Nagpal P, Young JC, Hagen G, Guilfoyle TJ, Reed JW. AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana. Development. 2005 Oct;132(20):4563-74. Epub 2005 Sep 21. PMID:16176952 doi:http://dx.doi.org/dev.02012

4ldv, resolution 1.45Å

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