The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
CtBP ligand motifs
Functional site description:
The C-terminal binding proteins (CtBP) are involved in multiple processes, including gene regulation, where they function as transcriptional corepressors by recruiting a repressor complex. CtBP itself is recruited to target genes by transcription factors belonging to diverse families through motif mediated interactions: the PxDLS motif that binds to a cleft on the substrate binding domain of CtBP, and the RRT motif that binds to a distinct surface cleft in the nucleotide binding domain of CtBP. These two binding sites are on opposite sides of a CtBP molecule, however in a CtBP homodimer the PxDLS binding site of one subunit is located adjacent to the RRT binding site of the other subunit, theoretically allowing binding of a ligand containing both motifs across the CtBP dimer.
ELMs with same func. site: LIG_CtBP_PxDLS_1  LIG_CtBP_RRT_2 
ELM Description:
The structure of a synthetic peptide derived from human Znf217 bound to CTBP1 from rat shows that the consensus RRT motif binds in a cleft on the surface of CtBP, defined mainly by the loop connecting α-helix C and β strand A, and by the α-helices F and G, which are all part of the nucleotide-binding domain. The side chains of the peptide residues R1, R2 and T3 are buried into a groove lined by CtBP residues Y129, A159, E164, H218, D220, R245, Q246, G247, A248, F249 and R274. The rest of the peptide lies at the protein surface and shows a kink at residues P6-P7, which causes the C-terminal residues to be located next to the last turn of alpha helix G (2HU2). The bound peptide adopts an extended conformation, antiparallel to α-helix G. The interaction is stabilised by salt bridges between R1 and D220 and between R2 and E164, hydrogen bonds between the residue pairs R1-H217, R2-G247, T3-D220, T3-R245 and G4-Q246, and intermolecular van der Waals interactions at P6 and P7 (Quinlan,2006). All the residues involved in binding and recognition of the peptide are conserved within the CtBP protein family, except for the conservative substitution of H218Q in CtBP2. Binding of the motif is not associated with significant tertiary/quaternary structural changes, except for some local side chain conformational changes, including replacement of the intramolecular salt bridge between R245 and D220 with the intermolecular R1-D220 interaction. The binding site for the PxDLS motif (LIG_CtBP_PxDLS_1) is situated on the opposite side of CtBP, however on the CtBP dimer the PxDLS binding site of one subunit is located on the same face as the RRT binding site of the other subunit. This means it would be possible for a protein containing both an RTT motif and a PxDLS motif, which are only 61 amino acids apart in Znf217, to contact both subunits and bind across a CtBP dimer (Quinlan,2006). The motif seems to be conserved only in Vertebrates.
Pattern: [RG]RT[GSAT].PP..
Pattern Probability: 0.0000015
Present in taxon: Vertebrata
Interaction Domain:
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain (IPR006140) A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related (Stochiometry: 1 : 1)
o See 5 Instances for LIG_CtBP_RRT_2
o Abstract
C-terminal binding protein (CtBP) was initially identified as a phosphoprotein associating with the C-terminus of adenovirus E1A transforming protein (Boyd,1993), and is highly conserved in Metazoa. The invertebrate genome contains a single CtBP gene (Drosophila CtBP protein, O46036), while the vertebrate genome encodes two paralogues, CtBP1 (Q13363) and CtBP2 (P56545), that show sequence and structural similarity, and perform both unique and redundant functions during animal development, likely due to differential expression depending on tissue and developmental stage (Chinnadurai,2002; 22745816). CtBPs act as transcriptional corepressors that regulate the expression of genes involved in development, differentiation, apoptosis, anoikis and oncogenesis by recruiting a corepressor complex to DNA (Stankiewicz,2014). However, they also display cytoplasmic and membrane associated functions, being involved in fission of Golgi membrane (Weigert,1999; Corda,2006).
Mammalian CtBPs contain four functional domains: two substrate binding domains (SBD), a dehydrogenase domain, and a disordered C-terminal region (Chen,2021). The dehydrogenase domain contains a nucleotide binding domain (NBD) that binds NAD+/NADH and provides dehydrogenase activity, allowing CtBPs to act as a metabolic and redox sensor, but this still needs further investigation (Kumar,2002). In addition, binding of NADH promotes dimerization of CtBP, which is required for transcriptional repression (Bhambhani,2011). Vertebrate CtBP1 and CtBP2 can homo- or heterodimerise, and CtBP dimers can simultaneously interact with two PxDLS-containing proteins, e.g. with a DNA binding protein and a repressor protein. The C-terminal domain contains a PDZ motif and sites for posttranslational modification, such as phosphorylation and SUMOylation, that regulate the functionality of CtBP (Chen,2021). Two structural elements of CtBP act as sites for cofactor recruitment. The first is a hydrophobic cleft in the N-terminal SBD that binds proteins containing a PxDLS motif, but also mediates PxDLS independent interactions. As it links CtBP with DNA binding factors and components of the corepressor complex, this binding site is essential for CtBP function (Kuppuswamy,2008). The PxDLS motif binds by β-augmentation to a groove on the CtBP surface (1HL3; 8ATI). In the known instances, positively charged residues are disfavoured preceding the core of the motif but are strongly favoured following, reflecting the electrostatic surface of CtBPs. The second interaction site is a distinct surface groove on the NBD that binds RRT motif containing proteins. This site is functionally redundant with the PxDLS binding site, and all proteins with an RRT motif also contain a PxDLS-like sequence (Quinlan,2006).
Over 30 transcription factors have been reported to recruit CtBP for transcriptional repression of various target genes, including pro-apoptotic genes such as Bax and Bik, and tumour suppressor genes like PTEN and BRCA1. Most of these factors bind through their PxDLS motif, however some lack an obvious PxDLS-like sequence, while others interact using both a PxDLS motif and an RRT motif. Interestingly, the intrinsically disordered protein RAI2 (retinoic acid-induced 2) has a pair of non-canonical ALDLS motifs that bind to CtBP (Werner,2015). Nuclear CtBP protein complexes consist of sequence specific DNA-binding proteins such as Krueppel-like factors (e.g. Klf3/12), zinc finger proteins (e.g. Znf217), zinc finger E-box-binding homeobox 1 and 2 (Zeb1/2) and Ras-responsive element-binding protein 1 (RREB-1), as well as enzymatic components that catalyse histone modification, including histone deacetylases (HDAC1/2), histone acetyltransferases (p300 and CBP), a histone methyltransferase complex comprised of G9a, GLP, Wiz and CDYL, and the histone lysine-specific demethylase LSD1, and finally corepressors, such as CoREST and LCoR, and auxiliary components including SUMO E3 ligases (HPC2, PIAS1 and Pc2) (Kuppuswamy,2008; Stankiewicz,2014).
Emerging evidence indicates involvement of CtBPs in the pathogenesis of several diseases (Chen,2021; Stankiewicz,2014). These proteins act as oncogenes in many different cancers, including colon, prostate, breast and ovarian cancers, by regulating genes that control different aspects of tumorigenesis and progression, including cell proliferation and apoptosis, migration, invasion, metastasis, and multidrug resistance. CtBPs suppress multiple pro-apoptotic genes (BAX, BIK, BIM and others), as well as several tumour suppressor genes (PTEN, p21, p16, BRCA1/2) involved in proliferation, adhesion, migration and invasion of cancer cells. In addition, CtBP downregulates E-cadherin in cancer cells, which promotes epithelial to mesenchymal transition, an important trait of metastasis (Chen,2021; Stankiewicz,2014). In addition to CtBPs acting as corepressors, evidence also suggests that they can activate transcription of some genes, including the oncogene Tiam1, and the gene for multidrug resistance protein 1 (MDR1) that contributes to chemoresistance (23264848; Mansoori,2017). More recently CtBPs have been implicated in inflammatory diseases such as acute lung injury, traumatic brain injury, osteoarthritis and chronic renal failure among others, likely due to direct or indirect upregulation of proinflammatory cytokine genes (Chen,2020). Dysregulated CtBP has also been linked to the progression of neurodegenerative diseases like Huntington disease (11739372). Given their involvement in tumorigenesis, cell survival, epithelial to mesenchymal transition, metastasis, neurodegeneration and inflammatory responses, pharmacological modulation of CtBP using several approaches could be beneficial in treatment of cancer and neurodegenerative diseases. Small molecules can be targeted to inhibit enzymatic activity, to interfere with dimerisation, or to inhibit PxDLS mediated interactions of CtBP with coregulators (Dcona,2017; Blevins,2015).
o 2 selected references:

o 6 GO-Terms:

o 5 Instances for LIG_CtBP_RRT_2
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
A2A7B5 Prdm2
731 739 SSRFKRRTSSPPSSPQHSPA TP 2 Mus musculus (House mouse)
Q3U0X6 Zfp217
746 754 SVLRNRRTGCPPALLGKDVP TP 2 Mus musculus (House mouse)
Q92618 ZNF516
814 822 FLSRSGRTGPPPALGGKECQ TP 2 Homo sapiens (Human)
Q13029 PRDM2
735 743 SSRFKRRTSSPPSSPQHSPA TP 2 Homo sapiens (Human)
O75362 ZNF217
752 760 SLLRSRRTGCPPALLGKDVP TP 3 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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