Modeling the Structure of Yeast MAT<i>α</i>1: An HMG-Box Motif with a C-Terminal Helical Extension

Abstract

The yeast MATα1 is required for the activation of α-specific genes in Saccharomyces cerevisiae and thus confers the α-cell identity of the yeast. MATα1 contains a domain called the α-domain which has significant sequence identity to the HMG-box family of proteins. A multiple sequence alignment of several α-domains and various structurally determined HMG-box domains have revealed that both domains possess very similar structural and functional residues. We found that the basic amino acids of the N-terminal loop, the intercalating hydrophobic residues of the first helix, and the hydrophobic residues required for interactions within the core of the protein are remarkably conserved in α-domains and HMG-box proteins. Our generated molecular models suggest that the first and third helix will be shorter and that the HMG-box core is not an isolated domain. The region beyond the conserved HMG-box motif contains an extended helical region for about 20 -30 amino acids. Structural models generated by comparative modeling and ab initio modeling reveal that this region will add two or more additional α-helices and will make significant contacts to helix III, II and I of the HMG-box core. We were able to illustrate how the extended α-domain would bind to DNA by merging of the α-domain and the LEF-1/DNA complex. The models we are reporting will be helpful in understanding how MATα1 binds to DNA with its partner MCM1 and activates transcription of α-specific genes. These models will also aid in future biophysical studies of MATα1 including the crystallization and structure determination.

A Network of HMG-box Transcription Factors Regulates Sexual Cycle in the Fungus Podospora anserina

“…Group A (Figure 2) included exclusively the mating-type transcription factors with an α1 domain, which was proposed to correspond to a new class of HMG-box [27], [54]. Group A formed a clade related to the MATA_HMG subfamily and contained FMR1 (Podan1).…”

The master regulator MAT1-1-1 of fungal mating binds to its targets via a conserved motif in the human pathogen Aspergillus fumigatus

“…The alpha-box domains and HMG domains of MAT proteins from ascomycetes exhibit similar functional and structural residues, therefore they might bind to DNA in a similar fashion ( Jackson et al 2013 ). Since eukaryotic HMG domains were shown to be sufficient for DNA binding ( Schlierf 2002 ; Jauch et al 2012 ), we hypothesized that the region of AfMAT1-1-1 encoding an alpha-box DNA-binding domain would be essential for the site-specific interaction with DNA.…”

The mating type transcription factor MAT1-1-1 from the fungal human pathogen Aspergillus fumigatus: synthesis, purification, and crystallization of the DNA binding domain

“…Recently, we characterized the DNA binding motif of MAT1-1-1 derived from promoter regions of several developmentally regulated genes, including the one for the pheromone receptor PreA (Ramšak et al ., 2021). Several attempts have been undertaken to crystallize MAT1-1-1-like proteins (Jackson et al ., 2013; Dyer et al ., 2016), however no successful report has been published anywhere. Here we report for the first time the purification and crystallization protocol that results in the formation of crystals of a fungal α1 domain in complex with its target preA-2 DNA.…”