Crystal structure of the reaction complex of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Thermotoga maritima refines the catalytic mechanism and indicates a new mechanism of allosteric regulation

• Published in: Journal of molecular biology Vol. 341; no. 2; pp. 455 - 466
• Main Authors: Shumilin, Igor A, Bauerle, Ronald, Wu, Jing, Woodard, Ronald W, Kretsinger, Robert H
• Format: Journal Article
• Language: English
• Published: England 06-08-2004
• Subjects: 3-Deoxy-7-Phosphoheptulonate Synthase; Aldehyde-Lyases - antagonists & inhibitors; Aldehyde-Lyases - chemistry; Aldehyde-Lyases - metabolism; Allosteric Regulation; BASIC BIOLOGICAL SCIENCES; Binding Sites; BIOCHEMISTRY; Cadmium - metabolism; CRYSTAL STRUCTURE; Crystallography, X-Ray; Feedback, Physiological; MATERIALS SCIENCE; national synchrotron light source; Phenylalanine - metabolism; Phosphoenolpyruvate - metabolism; Protein Conformation; Protein Subunits; REGULATIONS; Saccharomyces cerevisiae; Sugar Phosphates - metabolism; Thermotoga maritima; Thermotoga maritima - enzymology; Tyrosine - metabolism
• ISSN: 0022-2836; 0021-9258; 1083-351X
• DOI: 10.1016/j.jmb.2004.05.077

3-Deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHPS) catalyzes the first reaction of the aromatic biosynthetic pathway in bacteria, fungi, and plants, the condensation of phosphoenolpyruvate (PEP) and d-erythrose-4-phosphate (E4P) with the formation of DAHP. Crystals of DAHPS from Thermotoga maritima (DAHPS(Tm)) were grown in the presence of PEP and metal cofactor, Cd(2+), and then soaked with E4P at 4 degrees C where the catalytic activity of the enzyme is negligible. The crystal structure of the "frozen" reaction complex was determined at 2.2A resolution. The subunit of the DAHPS(Tm) homotetramer consists of an N-terminal ferredoxin-like (FL) domain and a (beta/alpha)(8)-barrel domain. The active site located at the C-end of the barrel contains Cd(2+), PEP, and E4P, the latter bound in a non-productive conformation. The productive conformation of E4P is suggested and a catalytic mechanism of DAHPS is proposed. The active site of DAHPS(Tm) is nearly identical to the active sites of the other two known DAHPS structures from Escherichia coli (DAHPS(Ec)) and Saccharomyces cerevisiae (DAHPS(Sc)). However, the secondary, tertiary, and quaternary structures of DAHPS(Tm) are more similar to the functionally related enzyme, 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDOPS) from E.coli and Aquiflex aeolicus, than to DAHPS(Ec) and DAHPS(Sc). Although DAHPS(Tm) is feedback-regulated by tyrosine and phenylalanine, it lacks the extra barrel segments that are required for feedback inhibition in DAHPS(Ec) and DAHPS(Sc). A sequence similarity search revealed that DAHPSs of phylogenetic family Ibeta possess a FL domain like DAHPS(Tm) while those of family Ialpha have extra barrel segments similar to those of DAHPS(Ec) and DAHPS(Sc). This indicates that the mechanism of feedback regulation in DAHPS(Tm) and other family Ibeta enzymes is different from that of family Ialpha enzymes, most likely being mediated by the FL domain.