Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-binding Protein (CBP) and p300

Abstract

The transcriptional coactivators CREB-binding protein (CBP) and p300 undergo a particularly rich set of interactions with disordered and partly ordered partners, as a part of their ubiquitous role in facilitating transcription of genes. CBP and p300 contain a number of small structured domains that provide scaffolds for the interaction of disordered transactivation domains from a wide variety of partners, including p53, hypoxia-inducible factor 1α (HIF-1α), NF-κB, and STAT proteins, and are the targets for the interactions of disordered viral proteins that compete with cellular factors to disrupt signaling and subvert the cell cycle. The functional diversity of the CBP/p300 interactome provides an excellent example of the power of intrinsic disorder to facilitate the complexity of living systems.

Keywords: IDP; IDR; STAT transcription factor; cAMP response element-binding protein (CREB); coupled folding and binding; hypoxia-inducible factor (HIF); intrinsically disordered protein; intrinsically disordered region; protein-protein interaction; structure-function; transcriptional activation; transcriptional coactivator; viral oncoprotein.

FIGURE 1.

Domain arrangement of CBP/p300. A, schematic diagram of the domain structure of CBP showing binding sites of proteins that are mentioned in this review. NRID, nuclear receptor interaction domain (disordered in the free state); TAZ1 and TAZ2, transcriptional adapter zinc binding motifs; KIX, partner of KID of CREB; CRD1, cyclin-dependent kinase inhibitor-reactive domain (disordered in the free state); BRD, bromodomain; CH2, cysteine-histidine-rich domain 2, incorporating a PHD domain and a RING finger domain (TAZ1 and ZZ-TAZ2 are sometimes termed CH1 and CH3 respectively); HAT, histone acetyltransferase domain, including a disordered regulatory loop; ZZ, dystrophin-like small zinc binding domain; NCBD, nuclear receptor coactivator binding domain, also called IBiD (molten globule in the free state). Box sizes correspond approximately to the lengths of the amino acid sequences belonging to each region. B, schematic representation of the overall structure of CBP/p300, incorporating the domain structures obtained by NMR for the CBP TAZ1 (24), KIX (4), ZZ (100), TAZ2 (23), and NCBD (18), as well as the x-ray crystal structure of the combined BRD, CH2, and HAT domains of p300 (62). Gray spheres in the TAZ1, CH2, ZZ, and TAZ2 structures represent Zn²⁺. SUMO, small ubiquitin-like modifier; pCREB, phosphorylated CREB.

FIGURE 2.

Schematic representation of the interactions of CBP/p300 domains with arrays of different transcription factors assembled at promoters for transcription of different genes. The ability of CBP and p300 to broker transcriptional coactivation at many different promoters is mediated both by the long disordered regions linking the structured interaction domains and by the promiscuous affinity of those domains for disordered transactivation domains of many gene-specific transcription factors.

FIGURE 3.

TAZ domain structures. A, surface representation of TAZ1, colored according to electrostatic potential (blue, positive; red, negative), in complex with the activation domain of CITED2 (green ribbon) (29). B, superposition of the structures of the activation domains of HIF-1α (26), CITED2 (29), STAT2 (25), and RelA (30). The structures are superimposed on a best fit of the TAZ1 domains, which are omitted for clarity. The portions of each partner protein are shown as follows: HIF-1α (Protein Data Bank (PDB) 1L8C; residues 776–826; red); CITED2 (1R8U; 220–260; green); STAT2 (2KA4; 788–838; cyan); and RelA (2LWW; 431–484; blue). The N and C termini of each construct are indicated. C, structures of IDRs bound to TAZ2. Superposition of the structures of TAZ2 in complex with STAT1 (PDB 2KA6 (25); residues 723–750; green); C/EBP (3T92 (36); 37–59; blue); p53 AD1 (2K8F (34); 14–29; orange); p53 AD2 (2MZD (35); 43–56; magenta); and ETAD1 (2MH0; 11–29; red) is shown. The yellow ribbon is derived from the x-ray crystal structure of free TAZ2 (3IO2 (33)), and shows the extended α₄ helix of a neighboring TAZ2 molecule (residues 1834–1819) in the crystal lattice. Structures were aligned on a best fit of the TAZ2 domains; the gray surface shows the TAZ2 structure from the STAT1 complex (PDB 2KA6 (25)).

FIGURE 4.

KIX complexes. A, superimposed structures of binary complexes of KIX with pKID (1KDX (4)) and c-Myb (1SB0 (42)). The backbone of KIX in complex with pKID (yellow) is colored dark blue, and the KIX backbone in complex with c-Myb (red) is colored light blue. B, superimposed structures of the KIX-c-Myb binary complex (KIX, yellow; c-Myb, pink; 1SB0 (42)) with the ternary complex KIX-c-Myb-MLL (KIX, light blue; c-Myb, red; MLL, green; 2AGH (43)). Allosteric changes in the ternary complex (a loop movement and the extension of the C-terminal helix) are shown in dark blue.