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PDBsum entry 1buo
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Gene regulation
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PDB id
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1buo
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the btb domain from plzf.
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Authors
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K.F.Ahmad,
C.K.Engel,
G.G.Privé.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
12123-12128.
[DOI no: ]
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PubMed id
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Abstract
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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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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.
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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.
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