Oligomeric interactions maintain active‐site structure in a noncooperative enzyme family

Abstract

The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo‐EM structures, and enzymological data, demonstrate that a conserved tetramer interface maintains the active‐site structure in one such class of proteins, the short‐chain dehydrogenase/reductase (SDR) superfamily. Phylogenetic comparisons support a significantly longer polypeptide being required to maintain an equivalent active‐site structure in the context of a single subunit. Oligomerization therefore enhances evolutionary fitness by reducing the metabolic cost of enzyme biosynthesis. The large surface area of the structure‐stabilizing oligomeric interface yields a synergistic gain in fitness by increasing tolerance to activity‐enhancing yet destabilizing mutations. We demonstrate that two paralogous SDR superfamily enzymes with different specificities can form mixed heterotetramers that combine their individual enzymological properties. This suggests that oligomerization can also diversify the functions generated by a given metabolic investment, enhancing the fitness advantage provided by this architectural strategy. image Many proteins form evolutionarily conserved oligomers in the absence of obvious functional interactions between subunits. Structural and phylogenetic analyses demonstrate that these interactions maintain active‐site structure in the short‐chain dehydrogenase/reductase superfamily. A cryo‐EM structure of a short‐chain dehydrogenase/reductase (SDR) superfamily enzyme shows dynamic opening of its tetramerization interface coupled to disordering of its active site. The same homotetramer structure is conserved in the vast majority of SDR superfamily enzymes with structures deposited in the PDB. The maintenance of active‐site structure using homooligomeric interactions enables a shorter protein subunit to form an active enzyme. Increased evolutionary fitness can therefore be conferred by homooligomeric interactions due to reduced metabolic investment.