PDBsum entry: 1xbr

Transcription/DNA

PDB id: 1xbr

Contents

Protein chains

184 a.a. *

DNA/RNA

Waters ×143

* Residue conservation analysis

PDB id:

1xbr

Name:

Transcription/DNA

Title:

T domain from xenopus laevis bound to DNA

Structure:

DNA (5'- d( Ap Ap Tp Tp Tp Cp Ap Cp Ap Cp Cp Tp Ap Gp Gp Tp G p Tp Gp Ap Ap Ap Tp T)-3'). Chain: c, d. Engineered: yes. Protein (t protein). Chain: a, b. Engineered: yes

Source:

Other_details: palindromic binding site of the t domain from an in vitro selection experiment. Xenopus laevis. African clawed frog. Organism_taxid: 8355. Tissue: embryo. Gene: xbra. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.215 R-free: 0.283

Authors:

C.W.Muller

Key ref:

C.W.Müller and B.G.Herrmann (1997). Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. Nature, 389, 884-888. PubMed id: 9349824 DOI: 10.1038/39929

Date:

16-Jul-97 Release date: 16-Jan-98

Protein chains

P24781  (BRAC_XENLA) -  Brachyury protein

Seq: 432 a.a.

Struc: 184 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription (2 terms)
• Biochemical function: transcription factor activity (1 term)

DOI no: 10.1038/39929

Nature 389:884-888 (1997)

PubMed id: 9349824

Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor.

C.W.Müller, B.G.Herrmann.

ABSTRACT

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.

Selected figure(s)

Figure 2.
Figure 2 Ribbon diagram of the T-domain dimer bound to DNA. Depicted are residues 39-221 of both monomers (strands and loops: red, helices: yellow) and the 24-mer DNA duplex (blue). Labels mark strands of the central immunoglobulin fold (A-G) and the two smaller lid-forming sheets (bee'/c'cfga). This figure and Fig. 3b, c were generated with the program Ribbons30. a, View perpendicular to the DNA axis with the dyad vertical; b, rotated by 90° around the DNA axis with respect to a.

Figure 3.
Figure 3 Ribbon diagram of the T-domain dimer bound to DNA. Depicted are residues 39-221 of both monomers (strands and loops: red, helices: yellow) and the 24-mer DNA duplex (blue). Labels mark strands of the central immunoglobulin fold (A-G) and the two smaller lid-forming sheets (bee'/c'cfga). This figure and Fig. 3b, c were generated with the program Ribbons30. a, View perpendicular to the DNA axis with the dyad vertical; b, rotated by 90° around the DNA axis with respect to a.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1997, 389, 884-888) copyright 1997.

Figures were selected by the author.