The crystal structure of dynamin

Ford, M.G.J.; Jenni, Simon; Nunnari, Jodi

doi:10.1038/nature10441

Cited by 246 publications

(328 citation statements)

References 42 publications

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“…Comparison of the dynamin tetramer with the filament-like arrangements observed in the crystal structures of dynamin 1 2,3 shows that the tetramer is bent, such that the angle between the outer stalks is changed by 20° (Fig. 1, 4a).…”

mentioning

confidence: 95%

“…3b), but not at the outer, non-assembled sides of the tetramer. Previous studies have shown that mutation of R399 in loop L2 S completely destroys higher-order assembly and dynamin function 2,3,11 . In our structure, R399 of an outer molecule forms salt bridges to E410 in α2 S and to E345 in L1N S in the outer and inner molecules of the opposite dimer, respectively.…”

mentioning

confidence: 98%

“…1, Extended Data Table 1). Indeed, the asymmetric unit of the crystal lattice contained a dynamin tetramer that did not form the filamentous superstructures seen for dynamin 1 2,3 .…”

mentioning

confidence: 99%

“…oligomerizing mutants led to crystal structures of dynamin 1 2,3 . However, the postulated higher-order assembly interface was not resolved in these structures leaving the oligomerization mechanism unaddressed.…”

mentioning

confidence: 99%

“…Each of the dimers assembles via the previously described interface 2 2,3,[12][13][14] (Fig. 1, Extended Data Fig.…”

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confidence: 99%

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Crystal structure of the dynamin tetramer

Reubold

Faelber

Plattner

et al. 2015

Nature

122

160

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The mechano-chemical protein dynamin is the prototype of the dynamin superfamily of large GTPases, which shape and remodel membranes in diverse cellular processes 1 .Dynamin forms predominantly tetramers in the cytosol, which oligomerize at the neck of clathrin-coated vesicles to mediate constriction and subsequent scission of the membrane 1 . Previous studies have described the architecture of dynamin dimers 2,3 , but the molecular determinants for dynamin assembly and its regulation have remained unclear. Here, we present the crystal structure of the nucleotide-free dynamin tetramer.Combining structural data with mutational studies, oligomerization measurements and molecular dynamics simulations, we suggest a mechanism of how oligomerization of dynamin is linked to the release of intramolecular auto-inhibitory interactions. We elucidate how mutations that interfere with tetramer formation and auto-inhibition can lead to the congenital diseases Charcot-Marie-Tooth neuropathy (CMT) 4 and centronuclear myopathy (CNM) 5 , respectively. Strikingly, the bent shape of the tetramer explains how dynamin assembles into a right-handed helical oligomer of defined diameter, which has direct implications for its function in membrane constriction.The three highly conserved vertebrate isoforms of dynamin contain five distinct domains (Extended Data Fig. 1a): an N-terminal GTPase (G) domain mediating nucleotide binding and hydrolysis, a bundle signaling element (BSE), a stalk, a pleckstrin homology (PH) domain involved in lipid binding, and a proline rich domain (PRD) mediating interaction with BAR-and SH3-domain containing scaffolding proteins 6 . To exert its function in clathrinmediated endocytosis (CME), dynamin assembles via the stalks into a helical array surrounding the necks of invaginating clathrin-coated pits (CCP) 7,8 . Dimerization of GTPbound G domains from neighboring helical rungs induces GTP hydrolysis 9 . The ensuing conformational changes are thought to be transmitted from the G domain via the BSE to the stalk resulting in a sliding motion of adjacent helix rungs, concomitant helix constriction 10 , and eventually membrane scission. The inherent tendency to form large assemblies at high protein concentrations has hampered crystallization of dynamin in the past. The use of non-3 oligomerizing mutants led to crystal structures of dynamin 1 2,3 . However, the postulated higher-order assembly interface was not resolved in these structures leaving the oligomerization mechanism unaddressed.We reasoned that an alternative assembly-affecting mutation, such as K361S in dynamin 3 11 , may disturb the oligomerization interface to a lesser extent than the previously used mutants. We obtained crystals of nucleotide-free dynamin 3-K361S lacking the PRD (dynamin 3(∆PRD)-K361S) that diffracted to 3.7 Å (Methods, Extended Data Fig. 1, Extended Data Table 1). Indeed, the asymmetric unit of the crystal lattice contained a dynamin tetramer that did not form the filamentous superstructures seen for dynamin 1 2,3 .The dynamin tetr...

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mentioning

confidence: 95%

mentioning

confidence: 98%

“…1, Extended Data Table 1). Indeed, the asymmetric unit of the crystal lattice contained a dynamin tetramer that did not form the filamentous superstructures seen for dynamin 1 2,3 .…”

mentioning

confidence: 99%

mentioning

confidence: 99%

“…Each of the dimers assembles via the previously described interface 2 2,3,[12][13][14] (Fig. 1, Extended Data Fig.…”

mentioning

confidence: 99%

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Crystal structure of the dynamin tetramer

Reubold

Faelber

Plattner

et al. 2015

Nature

122

160

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Invited review: Mechanisms of GTP hydrolysis and conformational transitions in the dynamin superfamily

2016

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Dynamin superfamily proteins are multidomain mechano‐chemical GTPases which are implicated in nucleotide‐dependent membrane remodeling events. A prominent feature of these proteins is their assembly‐ stimulated mechanism of GTP hydrolysis. The molecular basis for this reaction has been initially clarified for the dynamin‐related guanylate binding protein 1 (GBP1) and involves the transient dimerization of the GTPase domains in a parallel head‐to‐head fashion. A catalytic arginine finger from the phosphate binding (P‐) loop is repositioned toward the nucleotide of the same molecule to stabilize the transition state of GTP hydrolysis. Dynamin uses a related dimerization‐dependent mechanism, but instead of the catalytic arginine, a monovalent cation is involved in catalysis. Still another variation of the GTP hydrolysis mechanism has been revealed for the dynamin‐like Irga6 which bears a glycine at the corresponding position in the P‐loop. Here, we highlight conserved and divergent features of GTP hydrolysis in dynamin superfamily proteins and show how nucleotide binding and hydrolysis are converted into mechano‐chemical movements. We also describe models how the energy of GTP hydrolysis can be harnessed for diverse membrane remodeling events, such as membrane fission or fusion. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 580–593, 2016.

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Structural and functional characterization of the dominant negative P‐loop lysine mutation in the dynamin superfamily protein Vps1

et al. 2020

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Dynamin-superfamily proteins (DSPs) are large self-assembling mechanochemical GTPases that harness GTP hydrolysis to drive membrane remodeling events needed for many cellular processes. Mutation to alanine of a fully conserved lysine within the P-loop of the DSP GTPase domain results in abrogation of GTPase activity. This mutant has been widely used in the context of several DSPs as a dominant-negative to impair DSP-dependent processes.However, the precise deficit of the P-loop K to A mutation remains an open question. Here, we use biophysical, biochemical and structural approaches to characterize this mutant in the context of the endosomal DSP Vps1. We show that the Vps1 P-loop K to A mutant binds nucleotide with an affinity similar to wild type but exhibits defects in the organization of the GTPase active site that explain the lack of hydrolysis. In cells, Vps1 and Dnm1 bearing the P-loop K to A mutation are defective in disassembly. These mutants become trapped in assemblies at the typical site of action of the DSP. This work provides mechanistic insight into the widely-used DSP P-loop K to A mutation and the basis of its dominant-negative effects in the cell.

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The crystal structure of dynamin

Cited by 246 publications

References 42 publications

Crystal structure of the dynamin tetramer

Crystal structure of the dynamin tetramer

Invited review: Mechanisms of GTP hydrolysis and conformational transitions in the dynamin superfamily

Structural and functional characterization of the dominant negative P‐loop lysine mutation in the dynamin superfamily protein Vps1

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