1I8J

CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID

Summary for 1I8J

• Entry DOI: 10.2210/pdb1i8j/pdb
• Descriptor: PORPHOBILINOGEN SYNTHASE, ZINC ION, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: lyase, heme biosynthesis, magnesium, 4, 7-dioxosebacic acid
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 71715.08

Authors

Kervinen, J.,Jaffe, E.K.,Stauffer, F.,Neier, R.,Wlodawer, A.,Zdanov, A. (deposition date: 2001-03-14, release date: 2001-06-20, Last modification date: 2023-08-09)

Primary citation

Kervinen, J.,Jaffe, E.K.,Stauffer, F.,Neier, R.,Wlodawer, A.,Zdanov, A.
Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity.
Biochemistry, 40:8227-8236, 2001

PubMed Abstract: 4,7-Dioxosebacic acid (4,7-DOSA) is an active site-directed irreversible inhibitor of porphobilinogen synthase (PBGS). PBGS catalyzes the first common step in the biosynthesis of the tetrapyrrole cofactors such as heme, vitamin B(12), and chlorophyll. 4,7-DOSA was designed as an analogue of a proposed reaction intermediate in the physiological PBGS-catalyzed condensation of two molecules of 5-aminolevulinic acid. As shown here, 4,7-DOSA exhibits time-dependent and dramatic species-specific inhibition of PBGS enzymes. IC(50) values vary from 1 microM to 2.4 mM for human, Escherichia coli, Bradyrhizobium japonicum, Pseudomonas aeruginosa, and pea enzymes. Those PBGS utilizing a catalytic Zn(2+) are more sensitive to 4,7-DOSA than those that do not. Weak inhibition of a human mutant PBGS establishes that the inactivation by 4,7-DOSA requires formation of a Schiff base to a lysine that normally forms a Schiff base intermediate to one substrate molecule. A 1.9 A resolution crystal structure of E. coli PBGS complexed with 4,7-DOSA (PDB code ) shows one dimer per asymmetric unit and reveals that the inhibitor forms two Schiff base linkages with each monomer, one to the normal Schiff base-forming Lys-246 and the other to a universally conserved "perturbing" Lys-194 (E. coli numbering). This is the first structure to show inhibitor binding at the second of two substrate-binding sites.

PubMed: 11444968
DOI: 10.1021/bi010656k

Experimental method

X-RAY DIFFRACTION (1.9 Å)