Porphobilinogen Deaminase

Function

Porphobilinogen deaminase (PBGD) also known as Hydroxymethylbilane synthase, is a monomeric deaminase and is the third enzyme in the heme biosynthesis pathways in mammals^[1]. It catalyses the polymerization of four porphobilinogen molecules to yield hydroxymethylbilane, a precursor in the formation of Porphyrin^[2]. Porphobilinogen deaminases are able to form surprisingly stable enzyme-substrate complexes with up to four pyrrole substrates interacting with the active site, a feature unique to the group of enzymes^[3]. Dipyrromethane (DPM), a cofactor unique to porphobilinogen deaminases, is thought to stabilize these interactions at each of the two active domains^[2]. .

Human porphobilinogen deaminase complex with dipyrromethane cofactor (PDB code 3eq1).

PBGD is a monomeric three-domain polypeptide with each domain consisting of approximately 110 amino acids. The human variant has an additional 29 residue loop in domain three that extends hydrogen bonding across domains one and three while E.coli PBGD is lacking this extended loop ^[1]. In the active site, a unique molecule known as Dipyrromethane interacts with porphobilinogen and anchors it in place^[1]. DPM consists of two pyrole units disulfide-bound to CYS[242]^[4]. Ordered sulfate ions are also hydrogen bonded with Arg26 and Ser28 residues near the active site that are highly conserved amongst human and E.coli variants of PBGD^[1].

Although PBGD appears to have hydrogen bonding capabilities between two identical PBGD units, at physiological pH, these interactions account for a dimer interface of approximately 5% while average dimer interface between subunits is 16%^[1]. Therefore, it is generally assumed that this protein is active naturally as a monomeric enzyme, while the crystalline form is a homo-dimeric structure of two identical PBGD subunits^[1].

Mechanism

PBGD is responsible for the formation of hydroxymethylbilane (HMB) from four porphobilinogen (PBG) subunits^[2]. The enzyme is loaded with a single porphobilinogen that is covalently linked to the dipyrromethane cofactor^[5]. The remaining three PBG units are attached in a head-to-tail fashion to yield an early, linear, HMB precursor that is covalently linked to PBGD^[5]. The six pyrole unit compound is cleaved at the second pyrole, by water, to yield the final product, hydroxymethylbilane^[6].

Importance of hPBGD

Acute Intermittent Porphyria

Acute intermittent porphyria (AIP) is an autosomal dominant disorder (0.06% incidence rate in population) caused by a mutation in the hydroxymethylbilane synthase gene (HMBS)^[7]. The protein, responsible for the conversion of porphobilinogen (PBG) to hydroxymethylbilane (HMB) is less active in most affected individuals by approximately one-half normal activity^[7]. Defective PBGD, AIP, and can be diagnosed through the detection of increased concentrations of porphobilinogen (PBG) in urine as it remains unincorporated by the defective enzyme^[8].