PDBsum entry 1buo

Gene regulation

PDB id: 1buo

Contents

Protein chain

121 a.a. *

Waters ×129

* Residue conservation analysis

PDB id:

1buo

Name:

Gene regulation

Title:

Btb domain from plzf

Structure:

Protein (promyelocytic leukemia zinc finger protein plzf). Chain: a. Fragment: btb domain. Synonym: poz domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: b834(de3).

Biol. unit:

Dimer (from PDB file)

Resolution:

1.90Å R-factor: 0.212 R-free: 0.252

Authors:

K.F.Ahmad,C.K.Engel,G.G.Prive

Key ref:

K.F.Ahmad et al. (1998). Crystal structure of the BTB domain from PLZF. Proc Natl Acad Sci U S A, 95, 12123-12128. PubMed id: 9770450 DOI: 10.1073/pnas.95.21.12123

Date:

04-Sep-98 Release date: 14-Oct-98

Protein chain

Q05516  (ZBT16_HUMAN) -  Zinc finger and BTB domain-containing protein 16 from Homo sapiens

Seq: 673 a.a.

Struc: 121 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.95.21.12123

Proc Natl Acad Sci U S A 95:12123-12128 (1998)

PubMed id: 9770450

Crystal structure of the BTB domain from PLZF.

K.F.Ahmad, C.K.Engel, G.G.Privé.

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.

Selected figure(s)

Figure 3.
Fig. 3. View of one monomer displayed as a solvent accessible surface in GRASP (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 5 and 6, which form a groove on the underside of the monomer that accommodates 1' from the adjoining monomer. The entrance to this groove is lined with Ala-90 and Tyr-113.

Figure 4.
Fig. 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 a FASTA3 (38) search of the SWALL 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 using GRASP (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.

Figures were selected by an automated process.