Sutinen, A. | Search bioRxiv

bioRxiv2020

Structure of the complete dimeric human GDAP1 core domain provides insights into ligand binding and clustering of disease mutations

Charcot-Marie-Tooth disease (CMT) is one of the most common inherited neurological disorders. Despite the common involvement of ganglioside-induced differentiation-associated protein 1 (GDAP1) in CMT, the protein structure and function, as well as the pathogenic mechanisms, remain unclear. We determined the crystal structure of the complete human GDAP1 core domain, which shows a novel mode of dimerization within the glutathione S-transferase (GST) family. The long GDAP1-specific insertion forms an extended helix and a flexible loop. GDAP1 is catalytically inactive towards classical GST substrates. Through metabolite screening, we identified a ligand for GDAP1, the fatty acid hexadecanedioic acid, which is relevant for mitochondrial membrane permeability and Ca2+ homeostasis. The fatty acid binds to a pocket next to a CMT-linked residue cluster, increases protein stability, and induces changes in protein conformation and oligomerization. The closest homologue of GDAP1, GDAP1L1, is monomeric in its full-length form. Our results highlight the uniqueness of GDAP1 within the GST family and point towards allosteric mechanisms in regulating GDAP1 oligomeric state and function.

biochemistry↗

bioRxiv2020

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

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+.

biochemistry↗