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.1998 Oct 13;95(21):12123-8.
doi: 10.1073/pnas.95.21.12123.

Crystal structure of the BTB domain from PLZF

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Crystal structure of the BTB domain from PLZF

K F Ahmad et al. Proc Natl Acad Sci U S A..

Abstract

The BTB domain (also known as the POZ domain) is an evolutionarily conserved protein-protein interaction motif found at the N terminus of 5-10% of C2H2-type zinc-finger transcription factors, as well as in some actin-associated proteins bearing the kelch motif. Many BTB proteins are transcriptional regulators that mediate gene expression through the control of chromatin conformation. In the human promyelocytic leukemia zinc finger (PLZF) protein, the BTB domain has transcriptional repression activity, directs the protein to a nuclear punctate pattern, and interacts with components of the histone deacetylase complex. The association of the PLZF BTB domain with the histone deacetylase complex provides a mechanism of linking the transcription factor with enzymatic activities that regulate chromatin conformation. The crystal structure of the BTB domain of PLZF was determined at 1.9 A resolution and reveals a tightly intertwined dimer with an extensive hydrophobic interface. Approximately one-quarter of the monomer surface area is involved in the dimer intermolecular contact. These features are typical of obligate homodimers, and we expect the full-length PLZF protein to exist as a branched transcription factor with two C-terminal DNA-binding regions. A surface-exposed groove lined with conserved amino acids is formed at the dimer interface, suggestive of a peptide-binding site. This groove may represent the site of interaction of the PLZF BTB domain with nuclear corepressors or other nuclear proteins.

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Figures

Figure 1
Figure 1
Sequence alignment of selected BTB domains and the observed secondary structure of the PLZF BTB domain. TTK (Tramtrack) and GAGA factor areDrosophila proteins, and the others are human proteins. The numbering is according to PLZF, and the crystal structure consists of residues 6–126. Black and gray backgrounds are used to indicate identical and/or conserved residues found in at least 50% of the proteins at a given position. Residues in a 310 helix conformation are indicated by hatching. • indicates amino acids that are classified as buried in the PLZF BTB monomer according to the criteria of Rice and Eisenberg (23). Colored numbers represent the percentage of contribution of the residue to the buried interface surface in the dimer, rounded to the nearest integer (i.e., a value of “0” represents a contribution from 0.1 to 0.49%, values of 1 represent a contribution of 0.5–1.49%, etc.). Residues indicated with red numbers participate in the swapped or closed interface, and amino acids involved with the central open interface are labeled in blue. Residues 16–19 contribute to both and are not classified.
Figure 2
Figure 2
(A) Ribbon diagram of the PLZF BTB domain dimer. One monomer is colored red and the other blue. The secondary structure elements of one monomer are indicated, and the position of the conserved residue Asp-35 is labeled. In this view, the two halves of the dimer are related by a vertical twofold symmetry axis. This figure was generated with the graphical programsetor (24). (B) Schematic representation of the topology of the dimer. α-Helices are indicated by rectangles, and β-sheets by thick arrows. The symmetry related secondary structure elements are indicated with primes.
Figure 3
Figure 3
View of one monomer displayed as a solvent accessible surface ingrasp (26). The orientation is roughly the same as for the blue monomer in Fig. 2A. The surface buried upon dimer formation is indicated in magenta, and residues that contribute at least 2% of the buried surface of the dimer (Fig. 1) are labeled. Residues from the closed interface are indicated with arrows. Not shown in the diagram are the residues from β5 and α6, which form a groove on the underside of the monomer that accommodates β1′ from the adjoining monomer. The entrance to this groove is lined with Ala-90 and Tyr-113.
Figure 4
Figure 4
Sequence conservation in the exposed surface of the BTB dimer. (A) View in the same orientation as in Fig. 2A. (B) View looking directly down the twofold axis of the dimer. A multiple sequence alignment was constructed as follows: residues 6–126 of PLZF were used in afasta3 (38) search of theswall database (Nonredundant Protein sequence database including Swissprot, Trembl, and TremblNew) at the EMBL- European Bioinformatics Institute server (http://www2.ebi.ac.uk/fasta3). Entries with E score <0.1 were used for further processing. Identical and closely matching sequences were removed from the set, so that the no two pairs in the final set of 42 sequences had >88% sequence identity. The set was then aligned, and the sequence variability was calculated as the number of different amino acids present at each residue position. The sequence variability was then displayed on the solvent accessible surface of the dimer by usinggrasp (26). In this variability scoring scheme, a fully conserved residue is assigned a value of 1, and the maximum variability is 20. The only exposed, fully conserved residue in the structure is Asp-35, present in the center of the groove.
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