6Y88

IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP

Summary for 6Y88

• Entry DOI: 10.2210/pdb6y88/pdb
• Descriptor: Indole-3-glycerol phosphate synthase, Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase, 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE, ... (7 entities in total)
• Functional Keywords: tryptophan biosynthesis, carboxylyase, ba8-barrel, indole synthesis, lyase
• Biological source: Pseudomonas aeruginosa; More
• Total number of polymer chains: 8
• Total formula weight: 253506.26

Authors

Soderholm, A.,Selmer, M. (deposition date: 2020-03-03, release date: 2020-09-23, Last modification date: 2024-01-24)

Primary citation

Soderholm, A.,Newton, M.S.,Patrick, W.M.,Selmer, M.
Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa : Decarboxylation is not essential for indole formation.
J.Biol.Chem., 295:15948-15956, 2020

PubMed Abstract: In tryptophan biosynthesis, the reaction catalyzed by the enzyme indole-3-glycerol phosphate synthase (IGPS) starts with a condensation step in which the substrate's carboxylated phenyl group makes a nucleophilic attack to form the pyrrole ring of the indole, followed by a decarboxylation that restores the aromaticity of the phenyl. IGPS from has the highest turnover number of all characterized IGPS enzymes, providing an excellent model system to test the necessity of the decarboxylation step. Since the 1960s, this step has been considered to be mechanistically essential based on studies of the IGPS-phosphoribosylanthranilate isomerase fusion protein from Here, we present the crystal structure of IGPS in complex with reduced CdRP, a nonreactive substrate analog, and using a sensitive discontinuous assay, we demonstrate weak promiscuous activity on the decarboxylated substrate 1-(phenylamino)-1-deoxyribulose-5-phosphate, with an ∼1000× lower rate of IGP formation than from the native substrate. We also show that IGPS, at an even lower rate, can produce IGP from decarboxylated substrate. Our structure of IGPS has eight molecules in the asymmetric unit, of which seven contain ligand and one displays a previously unobserved conformation closer to the reactive state. One of the few nonconserved active-site residues, Phe in IGPS, is by mutagenesis demonstrated to be important for the higher turnover of this enzyme on both substrates. Our results demonstrate that despite IGPS's classification as a carboxy-lyase ( decarboxylase), decarboxylation is not a completely essential step in its catalysis.

PubMed: 32928960
DOI: 10.1074/jbc.RA120.014936

Experimental method

X-RAY DIFFRACTION (2.09983451737 Å)