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
The CtBP (C-terminal binding protein) protein is structurally related to dehydrogenases and is indeed a NAD-dependent dehydrogenase (Kumar,2002). It was originally discovered as a protein associating with adenovirus E1A. Deletion of a short region in E1A that was found to be essential for the interaction with CtBP resulted in increased transcriptional activity, suggesting that CtBP might be a co-repressor for E1A (Boyd,1993). Several eukaryotic proteins such as Hairy, Knirps, Ikaros, Polycomb and several zinc finger proteins interact with CtBP through a short motif with the consensus PxDLS (Chinnadurai,2002). CtBP interacts with the PxDLS motif through its dehydrogenase domain, in a NAD+ dependent manner. CtBP proteins dimerise (vertebrate CtBP1 and CtBP2 can homo- or heterodimerise) and can simultaneously interact with two PxDLS containing proteins, e.g. with a DNA binding protein and a repressor. Binding to NAD+/NADPH aids dimerisation and therefore CtBP is sensitive to nutritional status (Jack,2011). A second role for CtBP in Golgi membrane fission may not involve PxDLS motifs (Corda,2006). Interestingly, several zinc finger proteins such as RIZ and ZNF217 were found to contain a second motif mediating binding to CtBP, in addition to the typical PxDLS motif. This second motif, known as the RRT motif, binds to a separate surface on CtBP, distinct from the PxDLS binding cleft (Quinlan,2006).

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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