Evolution of Catalysis: 3′‐Phospho adenosine 5′‐phosphosulfate synthase (PAPSS) and Methionine gamma Lyase deaminase (Mgld) as an Experimental and Computational Model System

Abstract

Binding of substrate or ligand to a protein is the first common step between a receptor protein and an enzyme. However, the receptor protein usually bear low Kd, that is higher affinity towards the ligand. Whereas, many of the enzymes bear higher Km, that is relatively lower affinity. What is the criteria behind this distinction? The product, is the transformed substrate and it would have to leave the active site so that it can perform its function outside the binding pocket or it can be transformed further by a separate set (s) enzyme(s). Between this inter play, in a bifunctional enzyme, a product from one active site pocket is a substrate for the neighboring domain. Therefore, the product of domain [(1), ATP sulfurylase] is a substrate for the domain [(2) APS kinase], the new active site. This mandates that the active site 2 must have higher affinity (low Km) than that of the domain 1, so that it stays bound tighter and gets transformed into product 2. This would avoid futile cycle of substrate of domain 2 leaving back to be bound to domain 1 to become the substrate for the domain 1 backward reaction, or to occlude/inhibit. My data, from ATP sulfurylase (domain 1) and APS kinase (domain 2) of PAPSS kinetics proves the fundamentally perfected evolutionary concept. The computational data supports this concept as well. Afterall, nature rarely fails to achieve perfection and sophistication, especially after millions of years, as part of the evolutionary process. Certain enzymes like tryptophan synthetases have developed channeling as a means to perfect its overall efficiency of ultimate product formation. PAPSS is a good model system to address the binding energies, Km, Kcat. PAPSS is a standalone enzyme that binds to five different nucleotides ATP, AMP, ADP, APS, and PAPS. In addition, this enzyme binds to two different, a phospho and a sulfo nucleotides. Methionine gammalyase deaminase (Mgld) is a different example that use PLP as a coenzyme to assist catalysis. Mgld cleaves C‐S bond of methionine to form methylthiol and the PLP bound 2‐aminobutyrate is deaminated to form alpha‐keto butyrate. Here the active site is constrained and very little flexibility is observed. Thus, the evolution of enzyme active site catalysis will be discussed using PAPSS and Mgld systems.Support or Funding InformationN/AThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.