Fluorophore Placement and Size Impact E2 Ubiquitination Efficiency

E2 conjugating enzymes function in the ubiquitin-mediated proteolysis pathway by accepting ubiquitin (Ub) from an E1 enzyme (Uba1), forming an E2~Ub thioester conjugate, and transferring Ub to a substrate or to an E3 ligase enzyme. Fluorescent or affinity tags are often used as sensitive readouts for catalytic variability and specificity of E2 enzymes and their variants. Here we examined how the size or placement of fluorescent tags compromise Ub conjugation for the E2 enzymes UbcH7, UbcH5a and Ubc13. Large green fluorescent protein (GFP) based fluorophores were placed at the N- or C-terminus of the E2 enzyme UbcH7 and the N-terminus of Ub, and compared to Alexa-based dyes, approximately 30 times smaller, at the same positions. While all modified proteins formed E2~Ub conjugates, placing a smaller Alexa dye at the C-terminus of the E2 enzyme improves the initial rate of E2~Ub conjugate formation by up to 10-fold compared to a larger GFP-based tag (YPet) at the N-terminus. In the case of UbcH5a, YPet labelling at its N-terminus significantly slowed formation of an E2~Ub conjugate and Ub unloading to the HECT domain of HUWE1 when compared to UbcH7. Overall, we find that small Alexa dye-based tags, especially when placed at the C-terminus of E2 enzymes, are an optimal choice for monitoring E2 ubiquitination using fluorescence-based experiments.