2X6V image
Deposition Date 2010-02-22
Release Date 2010-04-28
Last Version Date 2024-11-06
Entry Detail
PDB ID:
2X6V
Title:
Crystal structure of human TBX5 in the DNA-bound and DNA-free form
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 61 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:T-BOX TRANSCRIPTION FACTOR TBX5
Gene (Uniprot):TBX5
Chain IDs:A, B
Chain Length:203
Number of Molecules:2
Biological Source:HOMO SAPIENS
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3'
Chain IDs:C
Chain Length:11
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3'
Chain IDs:D
Chain Length:11
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT
Primary Citation
Structural Basis of Tbx5-DNA Recognition: The T-Box Domain in its DNA-Bound and -Unbound Form.
J.Mol.Biol. 400 71 ? (2010)
PMID: 20450920 DOI: 10.1016/J.JMB.2010.04.052

Abstact

TBX5, a member of the T-box transcription factor family, plays an important role in heart and limb development. More than 60 single point or deletion mutations of human TBX5 are associated with Holt-Oram syndrome that manifests itself as heart and limb malformations in 1 out of 100,000 live births. The majority of these mutations are located in the TBX5 T-box domain. We solved the crystal structures of the human TBX5 T-box domain in its DNA-unbound form and in complex with a natural DNA target site allowing for the first time the comparison between unbound and DNA-bound forms. Our analysis identifies a 3(10)-helix at the C-terminus of the T-box domain as an inducible recognition element, critically required for the interaction with DNA, as it only forms upon DNA binding and is unstructured in the DNA-unbound form. Using circular dichroism, we characterized the thermal stability of six TBX5 mutants containing single point mutations in the T-box domain (M74V, G80R, W121G, G169R, T223M, and R237W) and compared them with wild-type protein. Mutants G80R and W121G show drastically reduced thermal stability, while the other mutants only show a marginal stability decrease. For all TBX5 mutants, binding affinities to specific and nonspecific DNA sequences were determined using isothermal titration calorimetry. All TBX5 mutants show reduced binding affinities to a specific DNA target site, although to various degrees. Interestingly, all tested TBX5 mutants differ in their ability to bind unspecific DNA, indicating that both sequence-specific and unspecific binding might contribute to the misregulation of target gene expression.

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