Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206

Abstract

Zfp206 (also named as Zscan10) belongs to the subfamily of C 2 H 2 zinc finger transcription factors, which is characterized by the N-terminal SCAN domain. The SCAN domain mediates self-association and association between the members of SCAN family transcription factors, but the structural basis and selectivity determinants for complex formation is unknown. Zfp206 is important for maintaining the pluripotency of embryonic stem cells presumably by combinatorial assembly of itself or other SCAN family members on enhancer regions. To gain insights into the folding topology and selectivity determinants for SCAN dimerization, we solved the 1.85 Å crystal structure of the SCAN domain of Zfp206. In vitro binding studies using a panel of 20 SCAN proteins indicate that the SCAN domain Zfp206 can selectively associate with other members of SCAN family transcription factors. Deletion mutations showed that the N-terminal helix 1 is critical for heterodimerization. Double mutations and multiple mutations based on the Zfp206SCAN–Zfp110SCAN model suggested that domain swapped topology is a possible preference for Zfp206SCAN–Zfp110SCAN heterodimer. Together, we demonstrate that the Zfp206SCAN constitutes a protein module that enables C 2 H 2 transcription factor dimerization in a highly selective manner using a domain-swapped interface architecture and identify novel partners for Zfp206 during embryonal development.

The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer

“…Moreover, we used the interaction partners, from I2D , for which at least one experimental structure was available in the PDB . We also included two additional SCAN domain proteins, the Zfp206 and Peg3 [PDB entries 4E6S (Liang et al, 2012) chain A and 4BHX (Rimsa et al, 2013) chain A, respectively] to further investigate the role of SCAN-mediated hetero-dimerization. For analyses, we retained only those complexes with a predicted docking energy lower than −2.39 kcal/mol (Figure 2).…”

Structure of the SCAN Domain of Human Paternally Expressed Gene 3 Protein

“…The ability of a SCAN domain to self-associate was first shown for ZNF174 using a mammalian two-hybrid system and subsequently heterodimer formation was also noted [23]. Our current understanding suggests that the presence of SCAN domains in some proteins carrying Cys 2 -His 2 Krüppel-type motifs allows them to interact in a combinatorial fashion to control gene expression [26].…”

“…These residues are highly conserved within SCAN domains and observed to form similar hydrogen bonding patterns where the structures are known. Furthermore, mutation of both the equivalent Arg50 and Arg61 residues to alanines in Zfp206 destabilizes heterodimerization with Zfp110 [26]. Thus, these invariant residues seem to play an important role in both homo- and heterodimerization.…”

“…The data were indexed and integrated with iMOSFLM [32] and scaled with AIMLESS from the CCP4 program suite [33]. The structure was solved by molecular replacement with PHASER [34] using a poly-Ala model of the SCAN domain dimer from the mouse zinc finger protein 206 (Zfp206, PDB code 4E6S [26]) that shares 38% sequence identity with the PEG3-SCAN domain. The output model was subjected to a round of rigid body and restrained refinement using REFMAC5 [35].…”

“…Previously, two NMR and two crystal structures of SCAN domains have revealed the structural topology, which is constructed around five α-helices [26]–[28]. The SCAN domain forms a dimer with structural homology, appearing like a domain-swapped assembly, to the C-terminal domain (CTD) of the retroviral capsid protein [27], which is critical for capsid dimerization and viral assembly [29].…”