4ldu

From Proteopedia

(Difference between revisions)

Revision as of 10:16, 4 August 2016

Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor 5

Structural highlights

4ldu is a 1 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:	4ldv, 4ldw, 4ldx, 4ldy
Gene:	ARF5, At1g19850, F6F9.10, IAA24, MP (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ARFE_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 activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity.^[1] ^[2] ^[3]

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^[4]

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
↑ Hardtke CS, Ckurshumova W, Vidaurre DP, Singh SA, Stamatiou G, Tiwari SB, Hagen G, Guilfoyle TJ, Berleth T. Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4. Development. 2004 Mar;131(5):1089-100. PMID:14973283 doi:http://dx.doi.org/10.1242/dev.00925
↑ Vidaurre DP, Ploense S, Krogan NT, Berleth T. AMP1 and MP antagonistically regulate embryo and meristem development in Arabidopsis. Development. 2007 Jul;134(14):2561-7. Epub 2007 Jun 6. PMID:17553903 doi:http://dx.doi.org/10.1242/dev.006759
↑ 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/4ldu"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor 5==
 <StructureSection load='4ldu' size='340' side='right' caption='[[4ldu]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ldv|4ldv]], [[4ldw|4ldw]], [[4ldx|4ldx]], [[4ldy|4ldy]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARF5, At1g19850, F6F9.10, IAA24, MP ([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=4ldu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ldu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ldu RCSB], [http://www.ebi.ac.uk/pdbsum/4ldu 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=4ldu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ldu OCA], [http://pdbe.org/4ldu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ldu RCSB], [http://www.ebi.ac.uk/pdbsum/4ldu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ldu 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 4ldu" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4ldu

From Proteopedia

Revision as of 10:16, 4 August 2016

Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor 5

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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