3gcc

From Proteopedia

(Difference between revisions)

Revision as of 06:10, 7 February 2016

SOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, 46 STRUCTURES

Structural highlights

3gcc 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.
Gene:	ATERF1 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

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/3gcc"

@@ Line 2: / Line 2: @@
 <StructureSection load='3gcc' size='340' side='right' caption='[[3gcc]], [[NMR_Ensembles_of_Models | 46 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gcc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GCC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gcc]] 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=3GCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GCC FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATERF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATERF1 ([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=3gcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gcc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gcc RCSB], [http://www.ebi.ac.uk/pdbsum/3gcc 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=3gcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gcc OCA], [http://pdbe.org/3gcc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gcc RCSB], [http://www.ebi.ac.uk/pdbsum/3gcc PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ERF1A_ARATH ERF1A_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:9756931</ref> <ref>PMID:11950980</ref>
+[[http://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]]
@@ Line 16: / Line 16: @@
     <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=3gcc ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 26: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3gcc" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arabidopsis thaliana]]
+[[Category: Arath]]
 [[Category: Allen, M D]]
 [[Category: Ohme-Takagi, M]]

3gcc

From Proteopedia

Revision as of 06:10, 7 February 2016

SOLUTION STRUCTURE OF THE GCC-BOX BINDING DOMAIN, NMR, 46 STRUCTURES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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