Structural analysis of the PATZ1 BTB domain homodimer

Abstract

PATZ1 is a ubiquitously expressed transcriptional repressor belonging to the ZBTB family that is functionally expressed in T lymphocytes. PATZ1 targets the CD8 gene in lymphocyte development and interacts with the p53 protein to control genes that are important in proliferation and in the DNA-damage response. PATZ1 exerts its activity through an N-terminal BTB domain that mediates dimerization and co-repressor interactions and a C-terminal zincfinger motif-containing domain that mediates DNA binding. Here, the crystal structures of the murine and zebrafish PATZ1 BTB domains are reported at 2.3 and 1.8 Å resolution, respectively. The structures revealed that the PATZ1 BTB domain forms a stable homodimer with a lateral surface groove, as in other ZBTB structures. Analysis of the lateral groove revealed a large acidic patch in this region, which contrasts with the previously resolved basic co-repressor binding interface of BCL6. A large 30-amino-acid glycine-and alanine-rich central loop, which is unique to mammalian PATZ1 amongst all ZBTB proteins, could not be resolved, probably owing to its flexibility. Molecular-dynamics simulations suggest a contribution of this loop to modulation of the mammalian BTB dimerization interface. ISSN 2059-7983 research papers 582 Piepoli et al. PATZ1 BTB domain homodimer Acta Cryst. (2020). D76, 581-593Figure 1Sequence alignment of BTB domains of ZBTB transcription factors identifies a unique central region in PATZ1 that is conserved in mammals. (a) Sequence alignment of PATZ1 BTB domains from selected vertebrate species. The unique central sequence of the A2/B3 loop that is conserved in mammals and is missing in fish and amphibians is indicated in bold. (b) Sequence alignment of selected human ZBTB proteins and their predicted secondary structure. The sequences of the human PATZ1 and cKrox BTB domains with their unique extra region between the A2 helix and B3 strand are shown above. The PATZ1 amino acids that correspond to this region without electron-density assignments from the crystal structure are shown in bold. Arrows and rods identify predicted conserved -strand and -helical regions. The eight BTB domains with solved structures are annotated on the left with their common names in addition to the ZBTB nomenclature. Shading, asterisks, colons and periods identify conserved residues according to the Clustal format. A consensus sequence is shown at the bottom, with the three predicted degron residues involved in BTB domain stability indicated by arrows. research papers Acta Cryst. (2020). D76, 581-593 Piepoli et al. PATZ1 BTB domain homodimer 583 research papers Acta Cryst. (2020). D76, 581-593 Piepoli et al. PATZ1 BTB domain homodimer 591

Sibling rivalry among the ZBTB transcription factor family: homo vs. heterodimers

“…As the PATZ1 A2/B3 loop is a feature only observed in mammals, this region, including D76 shows low conservation; Fig. S3 and Piepoli et al, 2020 6 . We surmised that the choice between homo and heterodimer formation may be driven by the relative stability of each alternative pair.…”

“…Furthermore, according to the BTB quality control hypothesis 42 , heterodimers can be targeted for degradation based on the identity of the N-terminal 1 sequence that forms a critical interface surface. In fact, we identified an N-terminal sequence in the PATZ1 crystal structure that preferentially stabilizes homodimeric structures 6 . The propensity of this region to result in aggregation that potentially targets BTB domains for degradation has also been observed in the BCL6 protein crystal structure, which can be used to as a means for co-crystallization 52 .…”

“…As the PATZ1 A2/B3 loop is a feature only observed in mammals, this region, including D76 shows low conservation (Fig. S3 and Piepoli et al, 2020 6 ).…”

“…In addition to mediating homodimerization, the BTB dimer forms a scaffold for other ligands that modify the transcriptional regulation of target genes 12 . We recently solved the crystal structure of one ZBTB family member, PATZ1 (ZBTB19 or MAZR) from mouse and zebrafish 6 . This work highlighted the similarity of the structures of known BTB domains.…”

“…The secondary structures are annotated on the sequences for orientation with part (a). The unlabeled -strand between A2 and B3 indicates an additional secondary structure revealed in the model of PATZ16 . Figure2.…”