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Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains

By Matti Myllykoski, Aleksi Sutinen, M. Kristian Koski, Juha P Kallio, Arne Raasakka, Johanna Myllyharju, Rik K. Wierenga, Peppi Koivunen

Posted 26 Oct 2020
bioRxiv DOI: 10.1101/2020.10.25.354423

Prolyl 4-hydroxylases (P4Hs) catalyze post-translational hydroxylation of peptidyl proline residues. In addition to collagen P4Hs and hypoxia-inducible factor P4Hs, a poorly characterized endoplasmic reticulum (ER)-localized transmembrane prolyl 4-hydroxylase (P4H-TM) is found in animals. P4H-TM variants are associated with the familiar neurological HIDEA syndrome. Here, the 3D structure of the soluble human P4H-TM was solved using X-ray crystallography. The structure revealed an EF-domain with two Ca2+-binding motifs inserted to the catalytic domain. A substrate-binding cavity was formed between the EF-domain and the catalytic domain. The active site contained bound Fe2+ and N-oxalylglycine. Comparison to homologous structures complexed with peptide substrates showed that the substrate interacting residues and the lid structure that folds over the substrate are conserved in P4H-TM. Differences to homologs were found in the extensive loop structures that surround the substrate-binding cavity and generate a negative surface charge. Ca2+-binding affinity of P4H-TM was determined to be within the range of physiological Ca2+concentration in the ER. The proximity of the EF-domain to the active site suggests that Ca2+-binding is relevant to the catalytic activity. P4H-TM was found both as a monomer and a dimer in solution, but the monomer-dimer equilibrium was not regulated by Ca2+. The solved 3D structure suggests that the HIDEA variants cause loss of P4H-TM function. In conclusion, P4H-TM shares key structural elements with the known P4Hs while possessing a unique property among the 2-oxoglutarate-dependent dioxygenases having an EF-domain and a catalytic activity potentially regulated by Ca2+.

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