The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
LEDGF/P75 IBD binding site
Functional site description:
Lens epithelium-derived growth factor/p75 (LEDGF/p75 or PSIP1) is a transcriptional co-activator involved in chromosome tethering. It functions as an adaptor between chromatin and cellular proteins and is exploited by viral proteins using this tethering property for their chromosomal attachment. IBD is an important binding site for both cellular proteins and viral integrase, especially from HIV-1 and other lentiviruses. Most of the cellular binding partners possess two IBD-binding regions (IBM1 and IBM2) connected by a variable loop region that together constitute the bipartite motif for LEDGF-IBD binding. Both regions are necessary for efficient binding and the affinity is fine-tuned by charged residues preceding IBM2. Since the same site on IBD is involved in binding to both MLL1-IBM2 and HIV-IN, it is an attractive target for developing novel therapeutics for leukemia and HIV.
ELM Description:
The composite motif formed by the regions IBM1 and IBM2 is essential for LEDGF-IBD binding. IBM1 is an α-helical region situated upstream of the charged linker region. Apart from fly JIL1, known LEDGF interacting proteins all have IBM1 for interacting with IBD. It contains three conserved bulky amino acid residues that anchor in the hydrophobic pocket created by α3, α4, and α5 of the IBD. In the Menin-MLL-LEDGF ternary complex (3U88), the helix is much longer and binds both Menin and LEDGF where the aromatic rings of Phe129 and Phe133 of MLL1 insert into a hydrophobic pocket formed by three LEDGF-IBD helices. Studies have shown that mutation of the highly conserved phenylalanine to alanine (F129A) completely abolished LEDGF binding (Huang,2012).
IBM2 is downstream of IBM1 and separated by a flexible linker containing many acidic residues and phosphorylatable serine/threonine that modulate the binding affinity. The IBM2 region is characterized by a core F.GF sequence with adjacent acidic residues and serine/threonine residues (Sharma,2018). The aromatic side chains of two phenylalanine residues make critical contacts and they are anchored between the two interhelical loops of the LEDGF/p75 IBD (amino acids I359 to D369 and K402 to M413). The aromatic ring of the first phenylalanine resides in a relatively shallow hydrophobic pocket and the second phenylalanine is buried in a deeper pocket. Tryptophan-131 of HIV-IN can occupy the first binding site (Cermakova,2014).
A Gly residue preceding the last phenylalanine is also found conserved and contributes to avoiding steric hindrance. There are several D/E residues that precede the core motif and are important for complex stabilization.
Pattern: [LFVIM].{2,3}[LIVCYFM][FW].{3,35}[EDST].{0,1}[EDST].{0,1}F[^G]GF
Pattern Probability: 5.331e-07
Present in taxon: Vertebrata
Interaction Domain:
Lens epithelium-derived growth factor, integrase-binding domain (IPR021567) Lens epithelium-derived growth factor (LEDGF), also known as transcriptional co-activator p75, is a chromatin-associated protein that protects cells from stress-induced apoptosis (Stochiometry: 1 : 1)
o See 9 Instances for LIG_LEDGF_IBM_1
o Abstract
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).
o 11 selected references:

o 10 GO-Terms:

o 9 Instances for LIG_LEDGF_IBM_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
1384 1400 SLHQLFEGESETESFYGFEE TP 6 Homo sapiens (Human)
Q15648 MED1
878 898 FGEEYFDESSQSGDNDDFKGF TP 4 Homo sapiens (Human)
Q03164 MLL
129 151 FRAVFGESGGGGGSGEDEQFLGF TP 16 Homo sapiens (Human)
473 491 IADIFGESGDEEEEEFTGFN TP 5 Homo sapiens (Human)
618 634 SLLDLFQTSEEKSEFLGFTS TP 3 Homo sapiens (Human)
13 29 EVADIFNAPSDDEEFVGFRD TP 6 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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