1wid: Difference between revisions

Latest revision as of 13:41, 9 May 2024

Solution Structure of the B3 DNA-Binding Domain of RAV1

Structural highlights

1wid is a 1 chain structure with sequence from Arabidopsis thaliana. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

RAV1_ARATH Binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'. May function as negative regulator of plant growth and development.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The B3 DNA binding domain is shared amongst various plant-specific transcription factors, including factors involved in auxin-regulated and abscisic acid-regulated transcription. Herein, we report the NMR solution structure of the B3 domain of the Arabidopsis thaliana cold-responsive transcription factor RAV1. The structure consists of a seven-stranded open beta-barrel and two alpha-helices located at the ends of the barrel and is significantly similar to the structure of the noncatalytic DNA binding domain of the restriction enzyme EcoRII. An NMR titration experiment revealed a DNA recognition interface that enabled us to propose a structural model of the protein-DNA complex. The locations of the DNA-contacting residues are also likely to be similar to those of the EcoRII DNA binding domain.

Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1.,Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S Plant Cell. 2004 Dec;16(12):3448-59. Epub 2004 Nov 17. PMID:15548737^[3]

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

References

↑ Kagaya Y, Ohmiya K, Hattori T. RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 1999 Jan 15;27(2):470-8. PMID:9862967
↑ Hu YX, Wang YX, Liu XF, Li JY. Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res. 2004 Feb;14(1):8-15. PMID:15040885 doi:https://dx.doi.org/10.1038/sj.cr.7290197
↑ Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell. 2004 Dec;16(12):3448-59. Epub 2004 Nov 17. PMID:15548737 doi:https://dx.doi.org/10.1105/tpc.104.026112

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kagaya Y, Ohmiya K, Hattori T. RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res. 1999 Jan 15;27(2):470-8. PMID:9862967

[2] Hu YX, Wang YX, Liu XF, Li JY. Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res. 2004 Feb;14(1):8-15. PMID:15040885 doi:https://dx.doi.org/10.1038/sj.cr.7290197

[3] Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell. 2004 Dec;16(12):3448-59. Epub 2004 Nov 17. PMID:15548737 doi:https://dx.doi.org/10.1105/tpc.104.026112

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Solution Structure of the B3 DNA-Binding Domain of RAV1==
-<StructureSection load='1wid' size='340' side='right'caption='[[1wid]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1wid' size='340' side='right'caption='[[1wid]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wid]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WID FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wid]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WID FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RAV1 ([https://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">Solution NMR</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=1wid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wid OCA], [https://pdbe.org/1wid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wid RCSB], [https://www.ebi.ac.uk/pdbsum/1wid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wid ProSAT], [https://www.topsan.org/Proteins/RSGI/1wid TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RAV1_ARATH RAV1_ARATH]] Binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'. May function as negative regulator of plant growth and development.<ref>PMID:9862967</ref> <ref>PMID:15040885</ref>
+[https://www.uniprot.org/uniprot/RAV1_ARATH RAV1_ARATH] Binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'. May function as negative regulator of plant growth and development.<ref>PMID:9862967</ref> <ref>PMID:15040885</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Inoue, M]]
+[[Category: Inoue M]]
-[[Category: Kigawa, T]]
+[[Category: Kigawa T]]
-[[Category: Structural genomic]]
+[[Category: Yamasaki K]]
-[[Category: Yamasaki, K]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Dna binding protein]]
-[[Category: Dna-binding domain]]
-[[Category: Rsgi]]

1wid: Difference between revisions

Latest revision as of 13:41, 9 May 2024

Solution Structure of the B3 DNA-Binding Domain of RAV1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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