6TP5

Crystal structure of human Transmembrane prolyl 4-hydroxylase

Summary for 6TP5

• Entry DOI: 10.2210/pdb6tp5/pdb
• Descriptor: Transmembrane prolyl 4-hydroxylase, CHLORIDE ION, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (11 entities in total)
• Functional Keywords: prolyl-4-hydroxylase, 2-oxoglutarate-binding protein, transmembrane protein, ef-hand, double-stranded beta helix, iron-binding protein, calcium-binding protein, hidea syndrome, oxidoreductase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 102370.33

Authors

Myllykoski, M.,Sutinen, A.,Koski, M.K.,Kallio, J.P.,Raasakka, A.,Myllyharju, J.,Wierenga, R.K.,Koivunen, P. (deposition date: 2019-12-12, release date: 2020-12-23, Last modification date: 2024-10-23)

Primary citation

Myllykoski, M.,Sutinen, A.,Koski, M.K.,Kallio, J.P.,Raasakka, A.,Myllyharju, J.,Wierenga, R.K.,Koivunen, P.
Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains.
J.Biol.Chem., 296:100197-100197, 2020

PubMed 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 Ca-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 Ca binding is relevant to the catalytic activity. Functional analysis demonstrated that Ca-binding affinity of P4H-TM is within the range of physiological Ca 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 Ca. The catalytic site contained bound Fe 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.

PubMed: 33334883
DOI: 10.1074/jbc.RA120.016542

Experimental method

X-RAY DIFFRACTION (2.25 Å)