LIG_LEDGF_IBM_1

LEDGF/P75 is a nuclear protein belonging to the family of Hepatoma-derived growth factors (HDGFs). It was initially identified as an RNA polymerase II coactivator and subsequently as an HIV-1 integrase (IN) binding protein and integration cofactor. It is a ubiquitously expressed nuclear transcription factor-type protein with a role in transcriptional regulation, autoimmunity, cell survival, and prevention of apoptosis (Llano,2009). It binds to chromatin tightly and tethers multiple unrelated protein complexes to the chromatin fibers. Both the N-terminal PWWP domain and the C-terminal integrase binding domain (IBD) of LEDGF are responsible for the chromosome tethering function and transcriptional regulation. The chromatin linkage is mainly mediated by the N-terminal PWWP domain and a pair of A/T hooks which is further stabilized by three charged regions (CR1 to CR3) (Llano,2006). The C-terminal integrase binding domain (IBD) acts as a binding site for a number of cellular proteins and viral proteins (Tesina,2015) and directs them to chromatin. Its chromatin-tethering ability is linked to at least two unrelated diseases – HIV infection and MLL-rearranged acute leukaemia (Murai,2014).
The C-terminal portion of LEDGF contains a protein binding scaffold known as the Integrase Binding Domain (IBD) because HIV integrase was this domain's first identified binding partner. IBD is composed of four main α-helices (α1, α2, α4, and α5) and a shorter helix α3, that connects the two hairpins formed by helices α1-α2 and α4-α5. (Cherepanov,2005). The HIV integrase is a folded protein and binds using a domain:domain interaction interface.
Later studies show that multiple structurally unrelated cellular proteins like MLL1, ASK, JPO2, IWS1, PogZ, and Drosophila JIL1 bind the IBD through evolutionarily conserved motif regions known as the IBD-binding motifs (IBMs) allowing them to attach the chromatin (Tesina,2015). The binding of these proteins to LEDGF/p75 is mutually exclusive. Most of the binding proteins contain a bipartite IBM with components IBM1 and IBM2 that are both required to achieve high-affinity binding to LEDGF. Both regions are separated by a variable length acidic linker region and form independent contacts with IBD. The IBM1 is an α-helical region, which packs onto the site formed by two C-terminal helices of the IBD. In the Menin-MLL-LEDGF complex, the helix is much longer and binds both Menin and LEDGF (Huang,2012). Whereas, IBM2 is a short F.GF motif and interacts with the IBD mainly through two phenylalanine side chains that occupy two interhelical loops of IBD (Murai,2014). It is likely that G is excluded from the unconserved position to avoid erroneous binding to nuclear pore FG-NUP proteins. Almost all the IBM2s are characterized by a proximal phosphorylatable serine/threonine residue and a number of acidic residues that contribute to an increase in charge density and binding affinity. Along with IBM2, the IBM1 and the linker phosphorylation sites are essential for tight binding and inducing leukaemogenesis as in the case of MLL1 Fusion Proteins (Sharma,2018). However, Drosophila JIL1 appears to lack the IBM1 for its two F.GF IBM2s.
HIV-IN is the only known IBD binding partner that does not have an IBM and its interaction surface partially overlaps with the IBM binding site. The N-terminal domain of HIV-IN interacts with the positively charged surface recognized by the IBM acidic linker and the catalytic core domain binds to part of hydrophobic pockets occupied by the FxGF motif (Cherepanov,2005; Sharma,2018). This differential mode of interaction enables HIV-IN to efficiently sequester IBD from the Menin-MLL complex and provides a mechanistic view for the precision treatment of Mixed-Lineage Leukaemia (Cermakova,2016).