This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4ldw

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 17:48, 4 August 2016

Crystal structure of the DNA Binding Domain of arabidopsis thaliana auxin response factor 1, P21 structure

Structural highlights

4ldw is a 2 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	4ldu, 4ldv, 4ldx, 4ldy
Gene:	ARF1, At1g59750, auxin response factor 1, F23H11.7 (ARATH)
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]

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^[3]

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

References

↑ 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
↑ 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
↑ 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. Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors. Cell. 2014 Jan 30;156(3):577-89. doi: 10.1016/j.cell.2013.12.027. PMID:24485461 doi:http://dx.doi.org/10.1016/j.cell.2013.12.027

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/4ldw"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the DNA Binding Domain of arabidopsis thaliana auxin response factor 1, P21 structure==
 <StructureSection load='4ldw' size='340' side='right' caption='[[4ldw]], [[Resolution|resolution]] 2.67&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ldu|4ldu]], [[4ldv|4ldv]], [[4ldx|4ldx]], [[4ldy|4ldy]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARF1, At1g59750, auxin response factor 1, 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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ldw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ldw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ldw RCSB], [http://www.ebi.ac.uk/pdbsum/4ldw PDBsum]</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=4ldw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ldw OCA], [http://pdbe.org/4ldw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ldw RCSB], [http://www.ebi.ac.uk/pdbsum/4ldw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ldw ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4ldw" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4ldw

From Proteopedia

Revision as of 17:48, 4 August 2016

Crystal structure of the DNA Binding Domain of arabidopsis thaliana auxin response factor 1, P21 structure

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox