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2ebi

From Proteopedia

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Arabidopsis GT-1 DNA-binding domain with T133D phosphomimetic mutation

Structural highlights

2ebi is a 1 chain structure with sequence from Arath. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2jmw
Gene:	T6J4.18 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TGT1_ARATH] Probable transcription factor that binds specifically to the core DNA sequence 5'-GGTTAA-3'. May act as a molecular switch in response to light signals.^[1] ^[2] ^[3]

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

GT-1 is a plant transcription factor that binds to one of the cis-acting elements, BoxII, which resides within the upstream promoter region of light-responsive genes. GT-1 was assumed to act as a molecular switch modulated through Ca(2+)-dependent phosphorylation/dephosphorylation in response to light signals. It was shown previously that the phosphorylation of threonine 133 in the DNA-binding domain (DBD) of GT-1 results in enhancement of the BoxII-binding activity. Interestingly, point mutation of Thr133 to Asp also enhances the BoxII-binding activity. Here, we report the solution structures of hypothetical trihelix DBDs of the wild-type (WT) and a phosphomimetic mutant (T133D) of GT-1. First, we demonstrated that the isolated DBD of GT-1 alone has the ability to bind to DNA, and that the T133D mutation of the isolated DBD can enhance the DNA-binding affinity. The structures of these DBDs turned out to be almost identical. The structural topology resembles that of Myb DBDs, but all alpha-helices are longer in GT-1. Our NMR titration experiments suggested that these longer alpha-helices yield an enlarged DNA-binding surface. The phosphorylation site is located at the N-terminus of the third alpha-helix. We built a structural model of the T133D DBD:BoxII complex with the program HADDOCK. The model resembles the structure of the TRF1 DBD:telomeric DNA complex. Interestingly, the model implies that the phosphorylated side chain may directly interact with the bases of DNA. On the basis of our findings, we propose a mechanism by which the DNA-binding activity toward BoxII of the phosphorylated GT-1 could be enhanced.

Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation.,Nagata T, Niyada E, Fujimoto N, Nagasaki Y, Noto K, Miyanoiri Y, Murata J, Hiratsuka K, Katahira M Proteins. 2010 Nov 1;78(14):3033-47. PMID:20717979^[4]

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

References

↑ Marechal E, Hiratsuka K, Delgado J, Nairn A, Qin J, Chait BT, Chua NH. Modulation of GT-1 DNA-binding activity by calcium-dependent phosphorylation. Plant Mol Biol. 1999 Jun;40(3):373-86. PMID:10437822
↑ Ayadi M, Delaporte V, Li YF, Zhou DX. Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors in Arabidopsis. FEBS Lett. 2004 Mar 26;562(1-3):147-54. PMID:15044016 doi:http://dx.doi.org/10.1016/S0014-5793(04)00222-4
↑ Hiratsuka K, Wu X, Fukuzawa H, Chua NH. Molecular dissection of GT-1 from Arabidopsis. Plant Cell. 1994 Dec;6(12):1805-13. PMID:7866025 doi:http://dx.doi.org/10.1105/tpc.6.12.1805
↑ Nagata T, Niyada E, Fujimoto N, Nagasaki Y, Noto K, Miyanoiri Y, Murata J, Hiratsuka K, Katahira M. Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation. Proteins. 2010 Nov 1;78(14):3033-47. PMID:20717979 doi:10.1002/prot.22827

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ebi"

@@ Line 1: / Line 1: @@
 ==Arabidopsis GT-1 DNA-binding domain with T133D phosphomimetic mutation==
-<StructureSection load='2ebi' size='340' side='right' caption='[[2ebi]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2ebi' size='340' side='right'caption='[[2ebi]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ebi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EBI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ebi]] 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=2EBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EBI FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2jmw|2jmw]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jmw|2jmw]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T6J4.18 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T6J4.18 ([https://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=2ebi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ebi OCA], [http://pdbe.org/2ebi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ebi RCSB], [http://www.ebi.ac.uk/pdbsum/2ebi PDBsum]</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=2ebi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ebi OCA], [https://pdbe.org/2ebi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ebi RCSB], [https://www.ebi.ac.uk/pdbsum/2ebi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ebi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TGT1_ARATH TGT1_ARATH]] Probable transcription factor that binds specifically to the core DNA sequence 5'-GGTTAA-3'. May act as a molecular switch in response to light signals.<ref>PMID:10437822</ref> <ref>PMID:15044016</ref> <ref>PMID:7866025</ref>
+[[https://www.uniprot.org/uniprot/TGT1_ARATH TGT1_ARATH]] Probable transcription factor that binds specifically to the core DNA sequence 5'-GGTTAA-3'. May act as a molecular switch in response to light signals.<ref>PMID:10437822</ref> <ref>PMID:15044016</ref> <ref>PMID:7866025</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eb/2ebi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eb/2ebi_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ebi ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 33: / Line 34: @@
 </StructureSection>
 [[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Hiratsuka, K]]
 [[Category: Ikeda, Y]]

2ebi

From Proteopedia

Current revision

Arabidopsis GT-1 DNA-binding domain with T133D phosphomimetic mutation

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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