Brachyury: Difference between revisions
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<StructureSection load='1xbr' size='400' side='right' scene= caption='T protein complex with DNA (PDB code [[1xbr]])'> | |||
=Introduction= | =Introduction= | ||
Two well-known orthologues of the <i>Homo sapiens</i> T protein are present in mice (Brachyury) and <i>Xenopus laevis</i> (Xbra). The homologue of T in mice, Brachyury, was the first T-box crystal structure to be determined. | Two well-known orthologues of the <i>Homo sapiens</i> '''T protein''' or '''T-box transcription factor T''' are present in mice ('''Brachyury''') and <i>Xenopus laevis</i> ('''Xbra'''). The homologue of T in mice, Brachyury, was the first T-box crystal structure to be determined. | ||
=Crystal structure ([[1xbr]])= | |||
=Crystal structure= | |||
The T-box region of the Brachyury protein was crystallised with a 24 bp palindromic DNA duplex as determined by <i>in vitro</i> PCR-based binding selection. It crystallised as a dimer; in one monomer residues 39-221 were visible out of a total of 226 residues, and in the other residues 39-222 were visible. Both monomers were bound to the DNA (unlike in the structure of [[TBX5]]) and interacted through a poorly conserved region of 250 Å<sup>2</sup>. The N-terminus of 38 residues and C-terminus of 4 residues were disordered in the crystal structure. Nevertheless, the crystallographic structure agrees with DNA footprinting experiments in terms of which bases are protected by the protein. | The T-box region of the Brachyury protein was crystallised with a 24 bp palindromic DNA duplex as determined by <i>in vitro</i> PCR-based binding selection. It crystallised as a dimer; in one monomer residues 39-221 were visible out of a total of 226 residues, and in the other residues 39-222 were visible. Both monomers were bound to the DNA (unlike in the structure of [[TBX5]]) and interacted through a poorly conserved region of 250 Å<sup>2</sup>. The N-terminus of 38 residues and C-terminus of 4 residues were disordered in the crystal structure. Nevertheless, the crystallographic structure agrees with DNA footprinting experiments in terms of which bases are protected by the protein. | ||
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The <i>Xenopus laevis</i> homologue of Brachyury, Xbra, has a known mutation of Lys149 which destroys DNA-binding activity. This is equivalent to Asn155 and Asn353 of Eomes and VegT respectively. | The <i>Xenopus laevis</i> homologue of Brachyury, Xbra, has a known mutation of Lys149 which destroys DNA-binding activity. This is equivalent to Asn155 and Asn353 of Eomes and VegT respectively. | ||
==Additional Resources== | |||
For additional information, see: [[Transcription and RNA Processing]] | |||
= 3D Structures of brachyury = | |||
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} | |||
[[7hi8]] - hBra T domain residues 39-224 - human<br /> | |||
[[7hi9]] - hBra T domain (mutant)<br /> | |||
[[6f58]], [[8cdn]] - hBra T domain residues 39-224 + DNA <br /> | |||
[[1h6f]] - hBra residues 101-291 + DNA <br /> | |||
[[6f59]] - hBra T domain (mutant) + DNA <br /> | |||
[[5qrf]], [[5qrg]], [[5qrk]] - hBra T domain + pyrazole derivative <br /> | |||
[[5qrh]], [[5qri]], [[5qrv]], [[5qry]], [[5qs7]], [[5qsg]], [[5qsj]] - hBra T domain + piperazine derivative <br /> | |||
[[5qrp]], [[5qrq]], [[5qs5]], [[5qsb]], [[5qsh]] - hBra T domain + piperidine derivative <br /> | |||
[[5qrj]], [[5qrr]], [[5qs0]] - hBra T domain + morpholine derivative <br /> | |||
[[7zk2]] - hBra T domain (mutant) + morpholine derivative <br /> | |||
[[5qrl]], [[5qro]], [[5qs6]], [[5qs8]], [[5qse]], [[5qt0]] - hBra T domain + pyridine derivative <br /> | |||
[[5qsd]] - hBra T domain + pyrimidine derivative <br /> | |||
[[5qrm]] - hBra T domain + oxazole derivative <br /> | |||
[[5qrw]] - hBra T domain + imidazole derivative <br /> | |||
[[5qs1]], [[5qs4]], [[5qs9]] - hBra T domain + thiazole derivative <br /> | |||
[[5qrn]] - hBra T domain + pyrrolidine derivative <br /> | |||
[[5qrs]], [[5qrz]], [[5qsl]] - hBra T domain + carboxamide derivative <br /> | |||
[[5qrt]] - hBra T domain + ethanamide derivative <br /> | |||
[[5qru]] - hBra T domain + glycinamide derivative <br /> | |||
[[5qs3]] - hBra T domain + acetamide derivative <br /> | |||
[[5qrx]], [[5qsa]] - hBra T domain + benzoate derivative <br /> | |||
[[5qsk]] - hBra T domain + acetate derivative <br /> | |||
[[5qs2]] - hBra T domain + thiourea derivative <br /> | |||
[[5qsf]] - hBra T domain + phenol derivative <br /> | |||
[[5qsi]] - hBra T domain + aniline derivative <br /> | |||
[[5qsc]], [[6zu8]] - hBra T domain + inhibitor <br /> | |||
[[7zl2]], [[8a7n]], [[8a10]] - hBra T domain + ligand<br /> | |||
[[7zkf]], [[8fmu]] - hBra T domain (mutant) + ligand<br /> | |||
[[1xbr]] - Bra T domain + DNA - frog<br /> | |||
<br /> | |||
</StructureSection> | |||
==Reference== | |||
<ref group="xtra">PMID:009349824</ref><ref group="xtra">PMID:015048824</ref><references group="xtra"/> | |||
[[Category:Topic Page]] | |||