Student Posters 51st Lorne Proteins Conference 2026

Structural characterisation of SIN3’s PAH domains and their interaction with MNT (#352)

Bhagya Mendis 1 2 , Cyrus Tan 1 2 , Ahmad Wardak 1 , Sean Smyth 1 , Hai Vu Nguyen 1 2 , Suzanne Cory 1 2 , Peter Czabotar 1 2 , Michelle Miller 1 2
  1. Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
  2. Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia

Deregulation of the transcriptional activator MYC is a well-known driver of 70% of human cancers, however, developing clinically effective inhibitors targeting MYC has been challenging due to the absence of druggable pockets 1,2. MNT, a member of the MYC transcriptional network, is an alternative target in MYC driven B and T-cell cancers, as it has been shown that the absence of MNT in these settings results in a reduction in lymphomagenesis 3,4. MNT functions as a transcriptional repressor by recruiting the SIN3-HDAC complex through binding to a PAH (paired amphipathic) domain of SIN3 3. SIN3’s interactions with MXD1, of the MXD family of proteins and a relative of MNT, have been well characterised; however not much is known about MNT’s interactions with the SIN3 PAH domains 5,6. Here we show that MNT binds tightly to the PAH2 domains of both mammalian SIN3 isoforms (SIN3A and SIN3B). Using NMR, we confirmed that MNT’s binding to the PAH2 domains occur through its SIN3 interacting domain (SID). Our crystal structure demonstrates that the MNT-SID binds between the α1 and α2 helices of the SIN3A PAH2 domain, similar to the MXD1-SID 6, forming only hydrophobic interactions with the PAH2 domain. Uniquely, we observe that Met-1 of the MNT-SID interacts at the top of the PAH2 binding groove, which is not seen with structures of the PAH2 domain and other reported SIN3 binders like MXD1 or HBP1 6,7. Due to SIN3’s role in recruiting HDACs, it has been reported to bind to many transcription factors through its PAH1 or PAH2 domain 5,6. Here we showed that the PAH1 domain only binds to SAP25 tightly, and to MNT very weakly. Of the reported PAH2 binders, only MXD family proteins and MNT bound to SIN3 PAH2 domains at  physiologically relevant binding affinities. Our findings provide the first characterisation of the interaction between SIN3 PAH2 domains and MNT and define the interaction network of the PAH1 and PAH2 domains of SIN3 isoforms.

 

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  5. Wan M S M, Muhammad R, Koliopoulos M G, Roumeliotis T I, Choudhary J S and Alfieri C (2023), “Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex”, Nature Comms. 14:2556.
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  7. Swanson K A, Knoepfler P S, Huang K, et al. (2004), “HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations”, Nat. Struct. Mol. Biol., 11:738-746.