8E0S

DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with DAHP Oxime in unbound:(bound)2:unbound conformations

Summary for 8E0S

• Entry DOI: 10.2210/pdb8e0s/pdb
• Descriptor: Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive, alpha-D-glucopyranose, DAHP Oxime, ... (5 entities in total)
• Functional Keywords: dahp synthase inhibitor, dahp oxime complex, lyase
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 4
• Total formula weight: 153432.85

Authors

Berti, P.J.,Junop, M.S.,Grainger, R. (deposition date: 2022-08-09, release date: 2022-10-12, Last modification date: 2023-10-18)

Primary citation

Balachandran, N.,Grainger, R.A.,Rob, T.,Liuni, P.,Wilson, D.J.,Junop, M.S.,Berti, P.J.
Role of Half-of-Sites Reactivity and Inter-Subunit Communications in DAHP Synthase Catalysis and Regulation.
Biochemistry, 61:2229-2240, 2022

PubMed Abstract: α-Carboxyketose synthases, including 3-deoxy-d-heptulosonate 7-phosphate synthase (DAHPS), are long-standing targets for inhibition. They are challenging targets to create tight-binding inhibitors against, and inhibitors often display half-of-sites binding and partial inhibition. Half-of-sites inhibition demonstrates the existence of inter-subunit communication in DAHPS. We used X-ray crystallography and spatially resolved hydrogen-deuterium exchange (HDX) to reveal the structural and dynamic bases for inter-subunit communication in DAHPS(Phe), the isozyme that is feedback-inhibited by phenylalanine. Crystal structures of this homotetrameric (dimer-of-dimers) enzyme are invariant over 91% of its sequence. Three variable loops make up 8% of the sequence and are all involved in inter-subunit contacts across the tight-dimer interface. The structures have pseudo-twofold symmetry indicative of inter-subunit communication across the loose-dimer interface, with the diagonal subunits B and C always having the same conformation as each other, while subunits A and D are variable. Spatially resolved HDX reveals contrasting responses to ligand binding, which, in turn, affect binding of the second substrate, erythrose-4-phosphate (E4P). The -terminal peptide, M1-E12, and the active site loop that binds E4P, F95-K105, are key parts of the communication network. Inter-subunit communication appears to have a catalytic role in all α-carboxyketose synthase families and a regulatory role in some members.

PubMed: 36197914
DOI: 10.1021/acs.biochem.2c00465

Experimental method

X-RAY DIFFRACTION (1.65 Å)