Structure of a mitochondrial fission dynamin in the closed conformation

Abstract

Dynamin 1-like proteins (DNM1-L) are mechanochemical GTPases that induce membrane fission in mitochondria and peroxisomes. Their mechanism depends on conformational changes driven by nucleotide and lipid cycling. Here we show the crystal structure of a mitochondrial fission dynamin (CmDnm1) from the algae Cyanidioschyzon merolae. Unlike other eukaryotic dynamin structures, CmDnm1 is in a hinge 1 closed conformation, with the GTPase domain compacted against the stalk. Within the crystal, CmDnm1 packs as a diamond-shaped tetramer that is consistent with an inactive off-membrane state. Crosslinking, photoinduced electron transfer assays, and electron microscopy verify these structures. In vitro, CmDnm1 forms concentration-dependent rings and protein-lipid tubes reminiscent of DNM1-L and classical dynamin with hinge 1 open. Our data provides a mechanism for filament collapse and membrane release that may extend to other dynamin family members. Additionally, hinge 1 closing may represent a key conformational change that contributes to membrane fission.

Onsite GTP fuelling via DYNAMO1 drives division of mitochondria and peroxisomes

“…This result supported the observation that downregulation of DYNAMO1 decreased Dnm1 assembly at mitochondrial division sites (Supplementary Figure 7i–l ). Dnm1 of C. merolae forms a tetramer with a diameter of ~10 nm in off-membrane state in vitro 36 , and Dnm1 molecules in the division machineries are most likely recruited from membrane-free Dnm1 pool within cytosol 19 , 25 . Thus, the presence of DYNAMO1 likely induces conformational changes to organize Dnm1 molecules into a highly ordered ring-like structure or stabilizes a ring-like structure at the division site.…”

The structural biology of the dynamin‐related proteins: New insights into a diverse, multitalented family

“…Like other Drps, cmDnm1 self‐assembles in vitro into curved filaments or closed rings in a concentration‐dependent manner. However, the crystal structure of cmDnm1 revealed a novel closed conformation (Figure C) . The conformation of the BSEs captured in this structure is, as in all nucleotide‐free dynamin structures, in the closed state.…”

“…Overall, the observed Hinge 1 rotation of 95° compared to the nucleotide‐free Drp1 structure allows the cmDnm1 GTPase domain and BSEs to fold against the Stalk helices. Furthermore, the back of the now‐closed Hinge 1 forms a novel large interface (named Interface 5) with the back of a symmetry‐related GTPase domain, of size 2359 å 2 , with the distal ends of two BSEs interacting across the symmetric interface (Figure C). As the basic building block of the crystal remains a cmDnm1 dimer, formed by the conserved interaction at Stalk Interface 2, each dimer also participates in two novel Hinge 1 interfaces, such that the closed conformation consists of a dimer of dimers, in a diamond‐shaped conformation.…”

“…It is conserved in Drp1, Dnm1, and Vps1 but partially conserved in Mx proteins. Hinge 1: In the paper describing the structure of Cyanidioschyzon merolae Dnm1 (cmDnm1), 18 Hinge 1 refers to the connections between the BSE and the Stalk. Hinge 1 therefore consists of two chains: the linkers between the C GTPase and Stalk α1 helices and the Stalk α4 and C GED helices.…”

Bacterial dynamin-like proteins reveal mechanism for membrane fusion

“…Nucleotide binding to MFN1 also induces a 77 °C movement of the HD1 domain with respect to the G-domain 14 , indicating a conserved conformational switch in membrane fusion DLPs. These large domain movements were not observed in structures of dynamin, but a recent study also from the lab of Harry Low reports a full length apo structure of the mitochondrial fission DLP Dnm1, with a closed hinge 1 leading to a compaction of the G-domain against the stalk, suggesting that hinge 1 closure could be a conserved feature in in DSF proteins 16 . The flick knife closure of fusion DLPs likely constitutes the powers stroke that brings opposing membranes in close proximity or allow membrane bending to promote fission (Fig.…”