Journal Article

Loop 7 of E2 Enzymes: An Ancestral Conserved Functional Motif Involved in the E2-Mediated Steps of the Ubiquitination Cascade

Coccetti, Paola, Arrigoni, Alberto, Vanoni, Marco, De Gioia, Luca, Papaleo, Elena, Casiraghi, Nicola

2012

Overview

The ubiquitin (Ub) system controls almost every aspect of eukaryotic cell biology. Protein ubiquitination depends on the sequential action of three classes of enzymes (E1, E2 and E3). E2 Ub-conjugating enzymes have a central role in the ubiquitination pathway, interacting with both E1 and E3, and influencing the ultimate fate of the substrates. Several E2s are characterized by an extended acidic insertion in loop 7 (L7), which if mutated is known to impair the proper E2-related functions. In the present contribution, we show that acidic loop is a conserved ancestral motif in E2s, relying on the presence of alternate hydrophobic and acidic residues. Moreover, the dynamic properties of a subset of family 3 E2s, as well as their binary and ternary complexes with Ub and the cognate E3, have been investigated. Here we provide a model of L7 role in the different steps of the ubiquitination cascade of family 3 E2s. The L7 hydrophobic residues turned out to be the main determinant for the stabilization of the E2 inactive conformations by a tight network of interactions in the catalytic cleft. Moreover, phosphorylation is known from previous studies to promote E2 competent conformations for Ub charging, inducing electrostatic repulsion and acting on the L7 acidic residues. Here we show that these active conformations are stabilized by a network of hydrophobic interactions between L7 and L4, the latter being a conserved interface for E3-recruitment in several E2s. In the successive steps, L7 conserved acidic residues also provide an interaction interface for both Ub and the Rbx1 RING subdomain of the cognate E3. Our data therefore suggest a crucial role for L7 of family 3 E2s in all the E2-mediated steps of the ubiquitination cascade. Its different functions are exploited thank to its conserved hydrophobic and acidic residues in a finely orchestrate mechanism.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Amino Acid Motifs / Amino Acid Sequence / Amino acids / Amino Acids - metabolism / Animals / Bioinformatics / Biology / Biotechnology / Catalysis / Cells (Biology) / Cluster Analysis / Conserved Sequence / Enzymes / Humans / Hydrophobic and Hydrophilic Interactions / Hydrophobicity / Molecular Dynamics Simulation / Molecular Sequence Data / Motion / Phosphorylation / Phylogenetics / Phylogeny / Principal components analysis / Protein Binding / Protein Stability / Protein Structure, Secondary / Protein Structure, Tertiary / Proteins / Recruitment / Residues / Simulation / Static Electricity / Substrates / Ubiquitin / Ubiquitin - metabolism / Ubiquitin-Conjugating Enzymes - chemistry / Ubiquitin-Conjugating Enzymes - metabolism / Ubiquitin-protein ligase / Ubiquitination