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 PxDLS motif pattern is based on the conservation of reported sequence instances together with the structure of the CtBP domain in complex with a PxDLS peptide (1HL3). Beta-augmentation at the sheet edge places the peptide sidechains in specific places on the CtBP surface. Pro at position 1 makes an H-bond to strand edge backbone and fits in a hydrophobic pocket that will not accommodate other residues (Gly with no side chain may be the least disruptive). Position 2 contributes to beta augmentation so that the semi-conserved sidechain is placed in a shallow hydrophobic pocket, which also allows Glu due to proximity of surface positive charge. Position 3 is most often Asp, probably due to favourable charged residue proximity but is surface accessible and accepts some changes. Position 4 contributes to beta augmentation so that the sidechain enters a deep hydrophobic groove that fits to Leu and would probably allow Met but reject most other residues. Position 5 has a Ser-Thr preference but appears to accept R (as in HDACs) and some other mostly small residues. Following the core peptide there are clear preferences for Lys or Arg but these are not a strict requirement. However the conserved GLDLSKK motif in Hic1 is reported to bind CtBP but lacks Pro: Therefore for Gly at position 1 which must weaken the interaction, the motif in ELM requires C-terminal positive charge compensation.
Pattern Probability: 0.0001173
Present in taxon: Metazoa
Interaction Domain:
2-Hacid_dh (PF00389) D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (Stochiometry: 1 : 1)
o See 32 Instances for LIG_CtBP_PxDLS_1
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 8 selected references:

o 8 GO-Terms:

o 32 Instances for LIG_CtBP_PxDLS_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P03254 Early E1A 32
279 283 EDLLNESGQPLDLSCKRPRP TP 5 Human adenovirus 2
56 60 GGGGSPSPVELRGALVGSVD TP 1 Homo sapiens (Human)
Q14526 HIC1
241 246 RRCSPLCGLDLSKKSPPGSA TP 1 Homo sapiens (Human)
O60315 ZEB2
859 863 SSENSDEPLNLTFIKKEFSN TP 1 Homo sapiens (Human)
O60315 ZEB2
815 819 SEELQAEPLDLSLPKQMKEP TP 1 Homo sapiens (Human)
O60315 ZEB2
785 789 SRSNTPSPLNLSSTSSKNSH TP 1 Homo sapiens (Human)
P70062 tcf7l1-a
545 549 LQALPLLQAQPLSLVTKSSD TP 1 Xenopus laevis (African clawed frog)
P70062 tcf7l1-a
469 473 THSEQAQPLSLTTKPEARAQ TP 1 Xenopus laevis (African clawed frog)
1163 1167 VGSDNDIPLDLAIKHSRPGP TP 1 Homo sapiens (Human)
425 429 SREAGEGPEDLADGGPLLYR TP 1 Homo sapiens (Human)
O00257 CBX4
472 476 LDSDLDEPIDLRCVKTRSEA TP 1 Homo sapiens (Human)
Q91647 cbx4
455 459 LDSDLDEPIDLRCVKSRCDS TP 1 Xenopus laevis (African clawed frog)
794 798 PGPAADGPIDLSKKPRRPLP TP 1 Homo sapiens (Human)
64 68 LMADQDSPLDLTVRKSQSEP TP 1 Homo sapiens (Human)
Q15583 TGIF1
153 157 DEDSMDIPLDLSSSAGSGKR TP 1 Homo sapiens (Human)
P35712 SOX6
424 428 KDEAAAQPLNLSSRPKTAEP TP 1 Homo sapiens (Human)
P17789 ttk
593 597 SGASTPPPPDLSGQNSNQSL TP 1 Drosophila melanogaster (Fruit fly)
P56524 HDAC4
48 52 QVAPSAVPMDLRLDHQFSLP TP 1 Homo sapiens (Human)
Q8C2B3 Hdac7
22 26 TPGSQPQPMDLRVGQRPTVE TP 1 Mus musculus (House mouse)
Q99N13 Hdac9
23 27 MGLEPISPLDLRTDLRMMMP TP 1 Mus musculus (House mouse)
P28166 zfh1
786 790 SLTREDQPLDLSVKRDPLTP TP 1 Drosophila melanogaster (Fruit fly)
P14003 h
318 322 RVPMEQQPLSLVIKKQIKEE TP 1 Drosophila melanogaster (Fruit fly)
P41970 ELK3
273 277 HDSDSLEPLNLSSGSKTKSP TP 1 Homo sapiens (Human)
Q13422 IKZF1
34 38 GDEPMPIPEDLSTTSGGQQS TP 1 Homo sapiens (Human)
829 833 SCLEMDVPIDLSKKCLSQSE TP 1 Homo sapiens (Human)
P48552 NRIP1
440 444 SSYSNCVPIDLSCKHRTEKS TP 1 Homo sapiens (Human)
P10734 kni
331 335 TVSAQEGPMDLSMKTSRSSV TP 1 Drosophila melanogaster (Fruit fly)
P57682 KLF3
61 65 SHGIQMEPVDLTVNKRSSPP TP 1 Homo sapiens (Human)
P37275 ZEB1
734 738 QEEPQVEPLDLSLPKQQGEL TP 1 Homo sapiens (Human)
Q99708 RBBP8
490 494 GDCVMDKPLDLSDRFSAIQR TP 1 Homo sapiens (Human)
O95600 KLF8
86 90 FSLPQVEPVDLSFHKPKAPL TP 1 Homo sapiens (Human)
Q03112 MECOM
584 588 PATSQDQPLDLSMGSRSRAS TP 1 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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