Porphobilinogen Deaminase

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 interacts with porphobilinogen and anchors it in place^[1]. DPM consists of two pyrole units disulfide-bound to CYS[242]^[4]. Ordered 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].

3D structures of porphobilinogen deaminase

Updated on 10-April-2014

3eq1 – hPBGD (mutant) + dipyrromethane cofactor – human

3ecr - hPBGD + dipyrromethane cofactor
1gtk, 2ypn, 1ah5, 1pda - EcPBGD + dipyrromethane cofactor – Escherichia coli
1ypn - EcPBGD (mutant) + dipyrromethane cofactor
4htg – PBGD – Arabidopsis thaliana
4mlq, 4mlv – PBGD – Bacillus megaterium

References

1. ↑ ^{1.0 1.1 1.2 1.3 1.4 1.5 1.6} Gill R, Kolstoe SE, Mohammed F, Al D-Bass A, Mosely JE, Sarwar M, Cooper JB, Wood SP, Shoolingin-Jordan PM. Structure of human porphobilinogen deaminase at 2.8 A: the molecular basis of acute intermittent porphyria. Biochem J. 2009 Apr 28;420(1):17-25. PMID:19207107 doi:10.1042/BJ20082077
2. ↑ ^{2.0 2.1 2.2} Jordan PM, Warren MJ. Evidence for a dipyrromethane cofactor at the catalytic site of E. coli porphobilinogen deaminase. FEBS Lett. 1987 Dec 10;225(1-2):87-92. PMID:3079571
3. ↑ Anderson PM, Desnick RJ. Purification and properties of uroporphyrinogen I synthase from human erythrocytes. Identification of stable enzyme-substrate intermediates. J Biol Chem. 1980 Mar 10;255(5):1993-9. PMID:7354069
4. ↑ A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274
5. ↑ ^{5.0 5.1} Lander M, Pitt AR, Alefounder PR, Bardy D, Abell C, Battersby AR. Studies on the mechanism of hydroxymethylbilane synthase concerning the role of arginine residues in substrate binding. Biochem J. 1991 Apr 15;275 ( Pt 2):447-52. PMID:2025226
6. ↑ A.R. Battersby, F.J. Leeper. Biosynthesis of the pigments of life: mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen III. Chern. Rev. 1990 Nov;90(7):1261-1274
7. ↑ ^{7.0 7.1} Whatley S.D., Roberts A.G., Llewellyn D.H., Bennett C.P., Garrett C, Elder G.H. (2000). Non-erythroid form of acute intermittent porphyria caused by promoter and frameshift mutations distant from the coding sequence of exon 1 of the HMBS gene. Hum. Genet. 107 (3): 243–248.
8. ↑ Aarsand AK, Petersen PH, Sandberg S. Estimation and application of biological variation of urinary delta-aminolevulinic acid and porphobilinogen in healthy individuals and in patients with acute intermittent porphyria. Clin Chem. 2006 Apr;52(4):650-6. PMID:16595824 doi:10.1373/clinchem.2005.060772