Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors

Abstract

The TFAP2 family regulates gene expression during differentiation, development, and organogenesis, and includes five homologs in humans. They all possess a highly conserved DNA binding domain (DBD) followed by a helix-span-helix (HSH) domain. The DBD-HSH tandem domain specifically binds to a GCC(N3)GGC consensus sequence, but the precise recognition mechanisms remain unclear. Here, we found that TFAP2 preferred binding to the GCC(N3)GGC sequence, and the pseudo-palindromic GCC and GGC motifs and the length of the central spacer between the two motifs determined their binding specificity. Structural studies revealed that the two flat amphipathic α-helical HSH domains of TFAP2A stacked with each other to form a dimer via hydrophobic interactions, while the stabilized loops from both DBD domains inserted into two neighboring major grooves of the DNA duplex to form base-specific interactions. This specific DNA binding mechanism controlled the length of the central spacer and determined the DNA sequence specificity of TFAP2. Mutations of the TFAP2 proteins are implicated in various diseases. We illustrated that reduction or disruption of the DNA binding ability of the TFAP2 proteins is the primary cause of TFAP2 mutation-associated diseases. Thus, our findings also offer valuable insights into the pathogenesis of disease-associated mutations in TFAP2 proteins.

Macroscopic inhibition of DNA damage repair pathways by targeting AP-2α with LEI110 eradicates hepatocellular carcinoma

“…LEI110 was previously reported as a selective pan-inhibitor of the HRASLS family of thiol hydrolases (i.e., PLA2G16, HRASLS2, RARRES3, and iNAT) 39 . Yet a stronger binding was observed in LEI110 with AP-2α (8J0L) 28 , compared with PLA2G16 (4Q95 40 ) in terms of docking scores in Chimera (Autodock Vina) and for molecular dynamics in the Desmond of Schrodinger (Fig. 3g , Supplementary Fig.…”

“…PDB files (8J0L 28 for human AP-2α and A0A286YD43 for mouse AP-2α) were downloaded from Alphafold2 ( https://www.alphafold.ebi.ac.uk/ ) imported to Chimera version 1.17.3 29 ( https://www.cgl.ucsf.edu/chimera/download.html ) and performed high throughput screening for the AP-2a. In brief, Dock Prep was performed in the AP-2a protein: bond orders were assigned, hydrogens were added, disulphide bonds were generated.…”

“…The structure for TFAP2A was available at AlphaFold ( https://www.alphafold.ebi.ac.uk/ ) under the accessionA0A286YD43 for mouse AP-2α. And the structure for AP-2α in human was acquired from PDB database under the accession 8J0L 28 . The numerical source data for graphs and charts in the manuscript was uploaded as Supplementary data 1 .…”

GET: a foundation model of transcription across human cell types

“…We found that Alphafold can reach an area under the receiver operating characteristic (AUROC) of 0.69 and an average precision (AUPR) of 0.41 (Supplementary Figure 8a). The accuracy of AlphaFold dimer prediction is exemplified by the perfectly aligned TFAP2A structure to experimental results 53 (Supplementary Figure 8b), even though there is no other similar template in PDB. With AlphaFold2's established ability to predict unseen multimer structures, we questioned whether the disordered region in the structure could fold upon binding to partners.…”

Transcription factor activating enhancer-binding protein 2ε (AP2ε) modulates phenotypic plasticity and progression of malignant melanoma

“…This is seen in Liu et al, were differences between AP2α and β could not be defined although these were observed e.g. in the Seberg in vivo study [ 10 , 54 ].…”