1gcc

From Proteopedia

(Difference between revisions)

Current revision

SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE

Structural highlights

1gcc is a 3 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, 1 model
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EF100_ARATH Acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. Involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways.^[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

The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.

A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.,Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M EMBO J. 1998 Sep 15;17(18):5484-96. PMID:9736626^[4]

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

References

↑ Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell. 2000 Mar;12(3):393-404. PMID:10715325
↑ Onate-Sanchez L, Singh KB. Identification of Arabidopsis ethylene-responsive element binding factors with distinct induction kinetics after pathogen infection. Plant Physiol. 2002 Apr;128(4):1313-22. PMID:11950980 doi:http://dx.doi.org/10.1104/pp.010862
↑ Hao D, Ohme-Takagi M, Sarai A. Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant. J Biol Chem. 1998 Oct 9;273(41):26857-61. PMID:9756931
↑ Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M. A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO J. 1998 Sep 15;17(18):5484-96. PMID:9736626 doi:10.1093/emboj/17.18.5484

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/1gcc"

@@ Line 1: / Line 1: @@
-[[Image:1gcc.gif|left|200px]]<br /><applet load="1gcc" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1gcc" />
-'''SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE'''<br />
-==Overview==
+==SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE==
-The 3D solution structure of the GCC-box binding domain of a protein from, Arabidopsis thaliana in complex with its target DNA fragment has been, determined by heteronuclear multidimensional NMR in combination with, simulated annealing and restrained molecular dynamic calculation. The, domain consists of a three-stranded anti-parallel beta-sheet and an, alpha-helix packed approximately parallel to the beta-sheet. Arginine and, tryptophan residues in the beta-sheet are identified to contact eight of, the nine consecutive base pairs in the major groove, and at the same time, bind to the sugar phosphate backbones. The target DNA bends slightly at, the central CG step, thereby allowing the DNA to follow the curvature of, the beta-sheet.
+<StructureSection load='1gcc' size='340' side='right'caption='[[1gcc]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1gcc]] is a 3 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=1GCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GCC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 1 model</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=1gcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gcc OCA], [https://pdbe.org/1gcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gcc RCSB], [https://www.ebi.ac.uk/pdbsum/1gcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gcc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EF100_ARATH EF100_ARATH] Acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. Involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways.<ref>PMID:10715325</ref> <ref>PMID:11950980</ref> <ref>PMID:9756931</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/gc/1gcc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1gcc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.
-==About this Structure==
+A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.,Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M EMBO J. 1998 Sep 15;17(18):5484-96. PMID:9736626<ref>PMID:9736626</ref>
-GCC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GCC OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA., Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M, EMBO J. 1998 Sep 15;17(18):5484-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9736626 9736626]
+</div>
+<div class="pdbe-citations 1gcc" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Allen, M.D.]]
+[[Category: Allen MD]]
-[[Category: Ohme-Takagi, M.]]
+[[Category: Ohme-Takagi M]]
-[[Category: Suzuki, M.]]
+[[Category: Suzuki M]]
-[[Category: Tateno, M.]]
+[[Category: Tateno M]]
-[[Category: Yamasaki, K.]]
+[[Category: Yamasaki K]]
-[[Category: complex (transcription factor/dna)]]
-[[Category: ethylene inducible]]
-[[Category: protein-dna complex]]
-[[Category: transcription factor]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:56:10 2007''

1gcc

From Proteopedia

Current revision

SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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