Abstract
Prolyl 4-hydroxylases (P4Hs) catalyze post-translational hydroxylation of peptidyl proline residues. In addition to collagen P4Hs and hypoxia-inducible factor P4Hs, a third P4H—the poorly characterized endoplasmic reticulum–localized transmembrane prolyl 4-hydroxylase (P4H-TM)—is found in animals. P4H-TM variants are associated with the familiar neurological HIDEA syndrome, but how these variants might contribute to disease is unknown. Here, we explored this question in a structural and functional analysis of soluble human P4H-TM. The crystal structure revealed an EF domain with two Ca2+-binding motifs inserted within the catalytic domain. A substrate-binding groove was formed between the EF domain and the conserved core of the catalytic domain. The proximity of the EF domain to the active site suggests that Ca2+ binding is relevant to the catalytic activity. Functional analysis demonstrated that Ca2+-binding affinity of P4H-TM is within the range of physiological Ca2+ concentration in the endoplasmic reticulum. P4H-TM was found both as a monomer and a dimer in the solution, but the monomer–dimer equilibrium was not regulated by Ca2+. The catalytic site contained bound Fe2+ and N-oxalylglycine, which is an analogue of the cosubstrate 2-oxoglutarate. Comparison with homologous P4H 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, whereas the extensive loop structures that surround the substrate-binding groove, generating a negative surface potential, are different. Analysis of the structure suggests that the HIDEA variants cause loss of P4H-TM function. In conclusion, P4H-TM shares key structural elements with other P4Hs while having a unique EF domain.
Highlights
Eukaryotic prolyl 4-hydroxylases (P4Hs) are enzymes that catalyze the post-translational hydroxylation of peptidyl– proline residues to 4-hydroxyproline (Fig. 1A)
All known P4Hs belong to the same enzyme superfamily of iron and 2oxoglutarate–dependent dioxygenases (2OGDDs). 2-oxoglutarate–dependent dioxygenase (2OGDD) are defined by the double-stranded β-helix (DSBH) fold of the catalytic domain, the shared mechanism of the enzymatic
The secondary structure elements indicated above the sequences are based on the crystal structure of the transmembrane prolyl 4-hydroxylase (P4H-TM) determined in this study
Summary
Eukaryotic prolyl 4-hydroxylases (P4Hs) are enzymes that catalyze the post-translational hydroxylation of peptidyl– proline residues to 4-hydroxyproline (Fig. 1A). The P4H-TM structure contains an EF domain with two EF hands between residues 190 and 251 (Fig. 4A). The function of these residues can be predicted based on the substrate-peptide containing P4H structures of Chlamydomonas reinhardtii P4H (Cr-P4H) and HIF-P4H-2 (Fig. 5).
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