Highlights

A theoretical model that explains fuzzy recognition for partially folding upon binding proteins is derived and experimentally tested.

We show that the toxin RnlA belongs to the broad family of HEPN RNases. RnlA undergoes large RnlB-induced conformational changes that result in two types of dimers with fundamentally different interfaces.

Our first output on the SOG1 function in collaboration with the VIB group of Lieven de Veylder. We show that CK2 operates through phosphorylation of the cell cycle checkpoint activator SOG1. In addition to yielding Al tolerance, CK2 and SOG1 inactivation prevents meristem exhaustion under Pi starvation, revealing the existence of a low Pi-induced cell cycle checkpoint that depends on the DNA damage activator ATM.

The corresponding structure is the graTA toxin-antitoxin complex. Autorepression of the graTA toxin-antitoxin modules involves the complex between GraA and GraT and is modulated by the presence of an intrinsically disordered N-terminal segment on the GraT toxin. The latter is also essential for its ribosome-dependent ribonuclease activity, making it a rare example of an enzyme with functional disorder.

The intrinsically disordered domain of Phd employs an entropic exclusion mechanism to prevent simultaneous high affinity binding of two Phd dimers to its operator. Folding upon binding of this IDP to Doc relieves this conformational stress and allows for an high affinity interaction.

We show that in contrast to earlier suggestions the translation inhibitor Doc as a kinase that phosphorylates elongation factor Tu. Doc is a Fic protein that binds ATP in an inverse mode, allowing the transfer of a phosphate group rather than a AMP moiety to its target.

We show that the coupled folding and binding can occur with picomolar affinity via a combination of specific intramolecular interactions that favor the final folded structure and a less specific set of intermolecular contacts that provide a desolvation entropy boost. The binding partner functions more as a facilitator than a mold to conform to.

Using a combination of biochemistry and structural biology we showed for the first time how the intrinsically disordered domain of Phd allows the toxin Doc to act either as a de-repressor or a co-repressor in a ratio-dependent fashion.