LIG_CtBP_RRT_2

CtBP ligand motifs

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.

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.

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)