6T8M

Prolyl Hydroxylase (PHD) involved in hypoxia sensing by Dictyostelium discoideum

Summary for 6T8M

• Entry DOI: 10.2210/pdb6t8m/pdb
• Descriptor: Prolyl 4-hydroxylase subunit alpha, NICKEL (II) ION, GLYCEROL, ... (6 entities in total)
• Functional Keywords: prolyl hydroxylase, oxygen sensing, 2-oxoglutarate and iron dependent oxygenase, oxidoreductase
• Biological source: Dictyostelium discoideum
• Total number of polymer chains: 3
• Total formula weight: 81967.03

Authors

Chowdhury, R.,McDonough, M.A.,Liu, T.,Clifton, I.J.,Schofield, C.J. (deposition date: 2019-10-24, release date: 2020-09-23, Last modification date: 2024-01-24)

Primary citation

Liu, T.,Abboud, M.I.,Chowdhury, R.,Tumber, A.,Hardy, A.P.,Lippl, K.,Lohans, C.T.,Pires, E.,Wickens, J.,McDonough, M.A.,West, C.M.,Schofield, C.J.
Biochemical and biophysical analyses of hypoxia sensing prolyl hydroxylases from Dictyostelium discoideum and Toxoplasma gondii .
J.Biol.Chem., 295:16545-16561, 2020

PubMed Abstract: In animals, the response to chronic hypoxia is mediated by prolyl hydroxylases (PHDs) that regulate the levels of hypoxia-inducible transcription factor α (HIFα). PHD homologues exist in other types of eukaryotes and prokaryotes where they act on non HIF substrates. To gain insight into the factors underlying different PHD substrates and properties, we carried out biochemical and biophysical studies on PHD homologues from the cellular slime mold, and the protozoan parasite, , both lacking HIF. The respective prolyl-hydroxylases (DdPhyA and TgPhyA) catalyze prolyl-hydroxylation of S-phase kinase-associated protein 1 (Skp1), a reaction enabling adaptation to different dioxygen availability. Assays with full-length Skp1 substrates reveal substantial differences in the kinetic properties of DdPhyA and TgPhyA, both with respect to each other and compared with human PHD2; consistent with cellular studies, TgPhyA is more active at low dioxygen concentrations than DdPhyA. TgSkp1 is a DdPhyA substrate and DdSkp1 is a TgPhyA substrate. No cross-reactivity was detected between DdPhyA/TgPhyA substrates and human PHD2. The human Skp1 E147P variant is a DdPhyA and TgPhyA substrate, suggesting some retention of ancestral interactions. Crystallographic analysis of DdPhyA enables comparisons with homologues from humans, , and prokaryotes, informing on differences in mobile elements involved in substrate binding and catalysis. In DdPhyA, two mobile loops that enclose substrates in the PHDs are conserved, but the C-terminal helix of the PHDs is strikingly absent. The combined results support the proposal that PHD homologues have evolved kinetic and structural features suited to their specific sensing roles.

PubMed: 32934009
DOI: 10.1074/jbc.RA120.013998

Experimental method

X-RAY DIFFRACTION (2.02 Å)