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==T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA==
==T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA==
<StructureSection load='1xbr' size='340' side='right' caption='[[1xbr]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='1xbr' size='340' side='right'caption='[[1xbr]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1xbr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XBR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XBR FirstGlance]. <br>
<table><tr><td colspan='2'>[[1xbr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XBR FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">XBRA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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=1xbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xbr OCA], [http://pdbe.org/1xbr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xbr RCSB], [http://www.ebi.ac.uk/pdbsum/1xbr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xbr ProSAT]</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=1xbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xbr OCA], [https://pdbe.org/1xbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xbr RCSB], [https://www.ebi.ac.uk/pdbsum/1xbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xbr ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/BRAC_XENLA BRAC_XENLA]] Involved in the transcriptional regulation of genes required for mesoderm formation and differentiation. Causes dorsal mesodermal differentiation of animal cap ectoderm when co-expressed with wnt8 and noggin. None of these molecules causes dorsal mesoderm formation when expressed alone. Establishes the left/right axis at early gastrula stage by directly up-regulating mesodermal expression of zic3.<ref>PMID:7906224</ref> <ref>PMID:11869292</ref>
[https://www.uniprot.org/uniprot/TBXT_XENLA TBXT_XENLA] Involved in the transcriptional regulation of genes required for mesoderm formation and differentiation (PubMed:11869292). Binds to the palindromic T site 5'-TTCACACCTAGGTGTGAA-3' DNA sequence (PubMed:11111039). Causes dorsal mesodermal differentiation of animal cap ectoderm when co-expressed with wnt8 and noggin (PubMed:7906224). None of these molecules causes dorsal mesoderm formation when expressed alone (PubMed:7906224). Establishes the left/right axis at early gastrula stage by directly up-regulating mesodermal expression of zic3 (PubMed:11869292).<ref>PMID:11111039</ref> <ref>PMID:11869292</ref> <ref>PMID:7906224</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1xbr 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=1xbr ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The mouse Brachyury (T) gene is the prototype of a growing family of so-called T-box genes which encode transcriptional regulators and have been identified in a variety of invertebrates and vertebrates, including humans. Mutations in Brachyury and other T-box genes result in drastic embryonic phenotypes, indicating that T-box gene products are essential in tissue specification, morphogenesis and organogenesis. The T-box encodes a DNA-binding domain of about 180 amino-acid residues, the T domain. Here we report the X-ray structure of the T domain from Xenopus laevis in complex with a 24-nucleotide palindromic DNA duplex. We show that the protein is bound as a dimer, interacting with the major and the minor grooves of the DNA. A new type of specific DNA contact is seen, in which a carboxy-terminal helix is deeply embedded into an enlarged minor groove without bending the DNA. Hydrophobic interactions and an unusual main-chain carbonyl contact to a guanine account for sequence-specific recognition in the minor groove by this helix. Thus the structure of this T domain complex with DNA reveals a new way in which a protein can recognize DNA.
Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor.,Muller CW, Herrmann BG Nature. 1997 Oct 23;389(6653):884-8. PMID:9349824<ref>PMID:9349824</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1xbr" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: African clawed frog]]
[[Category: Large Structures]]
[[Category: Muller, C W]]
[[Category: Xenopus laevis]]
[[Category: Dna-binding protein]]
[[Category: Muller CW]]
[[Category: Transcription factor]]
[[Category: Transcription-dna complex]]

Latest revision as of 11:49, 14 February 2024

T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNAT DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA

Structural highlights

1xbr is a 4 chain structure with sequence from Xenopus laevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TBXT_XENLA Involved in the transcriptional regulation of genes required for mesoderm formation and differentiation (PubMed:11869292). Binds to the palindromic T site 5'-TTCACACCTAGGTGTGAA-3' DNA sequence (PubMed:11111039). Causes dorsal mesodermal differentiation of animal cap ectoderm when co-expressed with wnt8 and noggin (PubMed:7906224). None of these molecules causes dorsal mesoderm formation when expressed alone (PubMed:7906224). Establishes the left/right axis at early gastrula stage by directly up-regulating mesodermal expression of zic3 (PubMed:11869292).[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.

See Also

References

  1. ↑ Sinha S, Abraham S, Gronostajski RM, Campbell CE. Differential DNA binding and transcription modulation by three T-box proteins, T, TBX1 and TBX2. Gene. 2000 Nov 27;258(1-2):15-29. PMID:11111039 doi:10.1016/s0378-1119(00)00417-0
  2. ↑ Kitaguchi T, Mizugishi K, Hatayama M, Aruga J, Mikoshiba K. Xenopus Brachyury regulates mesodermal expression of Zic3, a gene controlling left-right asymmetry. Dev Growth Differ. 2002 Feb;44(1):55-61. PMID:11869292
  3. ↑ Cunliffe V, Smith JC. Specification of mesodermal pattern in Xenopus laevis by interactions between Brachyury, noggin and Xwnt-8. EMBO J. 1994 Jan 15;13(2):349-59. PMID:7906224

1xbr, resolution 2.50Å

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