Porphobilinogen synthase: An equilibrium of different assemblies in human health

Abstract

Porphobilinogen synthase (PBGS) is an essential enzyme that catalyzes an early step in heme biosynthesis. An unexpected human PBGS quaternary structure dynamic drove the definition of morpheeins, which are protein multimers that dissociate, change shape, and re-assemble differently with functional consequences. Each PBGS monomer has two domains that can reposition through a hinge motion. Human PBGS exists in an equilibrium among high activity octamer, low activity hexamer, and low mole-fraction dimer in which the hinge motion occurs. The dimer conformation dictates the multimer architecture. An octamer-specific inter-subunit interaction responds to pH, resulting in a pH-dependence to the octamer-hexamer equilibrium. An inborn error of metabolism, ALAD porphyria, is caused by single amino acid substitutions that stabilize the hexamer relative to octamer. Drugs that stabilize the PBGS hexamer result in a drug side effect that can exacerbate porphyria. PBGS is essential for all organisms that require respiration, photosynthesis, or methanogenesis. Consequently, phylogenetic variation in PBGS multimerization equilibria provides insight into how Nature has harnessed oligomeric variation in the control of protein function. The dynamic multimerization of PBGS revealed the morpheein mechanism for allostery, a structural basis for inborn errors of metabolism, a quaternary structure focus for drug discovery and/or drug side effects, and a pathway toward new antibiotics or herbicides. The fortuitous discovery of PBGS quaternary structure dynamics arose from characterization of a low-activity single amino acid variant that dramatically stabilized the hexamer, whose existence had previously gone unnoticed.

In Silico Exploration of Mycobacterium tuberculosis Metabolic Networks Shows Host-Associated Convergent Fluxomic Phenotypes

“…All the members of A1, A3 and A4 are affected by different potentially deleterious SNPs in this gene. HemB protein participates in an early step of the synthesis of cobalamin and mycobactins, among other compounds [34,[62][63][64]. Cobalamin is a cofactor of many enzymes and regulates gene expression [34].…”

Manipulation of a Cation-π Sandwich Reveals Conformational Flexibility in Phenylalanine Hydroxylase

“…Third, in the transition from a conformation wherein the ACT domain is docked to the catalytic domain of one neighboring subunit to a distant location wherein the ACT domain is docked to the ACT domain of a different neighboring subunit must involve a pathway during which the ACT domain is not docked to either neighboring subunit. Like the reported behavior of human porphobilinogen synthase, this is another example where single amino acid substitutions dramatically alter the conformational space sampled by a medically relevant protein and unmask structural conformers that are, in the wild type protein, too short-lived or in low abundance for extensive characterization (48,49). These variants can also provide a glimpse into the aberrant conformational sampling of disease-associated variants.…”

Wrangling Shape-Shifting Morpheeins to Tackle Disease and Approach Drug Discovery

“…The morpheein model of protein allostery is a dissociative allosteric model most closely related to the equilibrium models of Nussinov (e.g., Kar et al, 2010) and Hilser (e.g., Motlagh et al, 2014), with the added dimension of quaternary structure. In the prototype morpheein described below, porphobilinogen synthase, the alternate functions are high activity (on) vs. low activity (off) (Jaffe and Stith, 2007;Jaffe and Lawrence, 2014;Jaffe, 2016Jaffe, , 2020. In the Ebola virus VP40 protein, the alternate functions are entirely separate activities, each one of which is essential for the viral life cycle (Bornholdt et al, 2013).…”