The “Recognition Helix” of the Type II Acyl Carrier Protein (ACP) Utilizes a “Ubiquitin Interacting Motif (UIM)”-like Surface To Bind Its Partners

Abstract

Interaction interfaces comprise a finite number of sequence/structural motifs, which are often repeated in nature. Here we show how a helical motif present in the acyl carrier protein (ACP), involved in multiprotein interactions, displays a binding interface similar to that of the "ubiquitin interacting motif (UIM)". Analysis of the crystal structures of the ACP-enzyme complexes gave the first hint that helix II of the ACP ("universal recognition helix") utilizes UIM-like noncovalent interactions to associate with the type II fatty acid biosynthesis (FAS) pathway enzymes. The ACP interacting functional surface of the FAS enzymes comprises positively charged residues, flanking a central hydrophobic patch, akin to ubiquitin. Our nuclear magnetic resonance chemical shift perturbation studies, relaxation studies, and surface plasmon resonance measurements unequivocally show that helix II of ACP behaves like a UIM motif in its interactions with ubiquitin, by binding the Ile 44 functional surface of the latter. A synthetic peptide with the ACP helix II sequence showed equivalent binding to ubiquitin. The evolution of similar interaction motifs in the two systems has probably been driven by functional constraints, as both ACP and UIM participate in multiprotein interactions.