Summary: Dynamin central region
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Dynamin Edit Wikipedia article
Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin I from Rattus norvegicus
|Dynamin central region|
Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin I from Rattus norvegicus
Dynamin is a GTPase responsible for endocytosis in the eukaryotic cell. Dynamin is part of the "dynamin superfamily", which includes classical dynamins, dynamin-like proteins, Mx proteins, OPA, mitofusins, and GBPs. Members of the dynamin family are principally involved in the scission of newly formed vesicles from the membrane of one cellular compartment and their targeting to, and fusion with, another compartment, both at the cell surface (particularly caveolae internalization) as well as at the Golgi apparatus. Dynamin family members also play a role in many processes including division of organelles, cytokinesis and microbial pathogen resistance.
Dynamin itself is a 96 kDa enzyme, and was first isolated when researchers were attempting to isolate new microtubule-based motors from the bovine brain. Dynamin has been extensively studied in the context of clathrin-coated vesicle budding from the cell membrane. Beginning from the N-terminus, Dynamin consists of a GTPase domain connected to a helical stalk domain via a flexible neck region containing a Bundle Signalling Element and GTPase Effector Domain. At the opposite end of the stalk domain is a loop that links to a membrane-binding Pleckstrin homology domain. The protein strand then loops back towards the GTPase domain and terminates with a Proline Rich Domain that binds to the Src Homology domains of many proteins.
During clathrin-mediated endocytosis, the cell membrane invaginates to form a budding vesicle. Dynamin binds to and assembles around the neck of the endocytic vesicle, forming a helical polymer arranged such that the GTPase domains dimerize in an asymmetric manner across helical rungs. The polymer constricts the underlying membrane upon GTP binding and hydrolysis via conformational changes emanating from the flexible neck region that alters the overall helical symmetry. Constriction around the vesicle neck leads to the formation of a hemi-fission membrane state that ultimately results in membrane scission. Constriction may be in part the result of the twisting activity of dynamin, which makes dynamin the only molecular motor known to have a twisting activity.
In mammals, three different dynamin genes have been identified with key sequence differences in their Pleckstrin homology domains leading to differences in the recognition of lipid membranes:
- Dynamin I is expressed in neurons and neuroendocrine cells
- Dynamin II is expressed in most cell types
- Dynamin III is strongly expressed in the testis, but is also present in heart, brain, and lung tissue.
Mutations in Dynamin II have been found to cause dominant intermediate Charcot-Marie-Tooth disease. Epileptic encephalopathyâ€“causing de novo mutations in dynamin have been suggested to cause dysfunction of vesicle scission during synaptic vesicle endocytosis.
- Henley JR, Cao H, McNiven MA (December 1999). "Participation of dynamin in the biogenesis of cytoplasmic vesicles". FASEB Journal. 13 Suppl 2 (9002): S243â€“7. doi:10.1096/fasebj.13.9002.S243. PMID 10619136.
- Hinshaw, J. "Research statement, Jenny E. Hinshaw, Ph.D." National Institute of Diabetes & Digestive & Kidney Diseases, Laboratory of Cell Biochemistry and Biology. Accessed 19 March 2013.
- Urrutia R, Henley JR, Cook T, McNiven MA (January 1997). "The dynamins: redundant or distinct functions for an expanding family of related GTPases?". Proceedings of the National Academy of Sciences of the United States of America. 94 (2): 377â€“84. doi:10.1073/pnas.94.2.377. PMC 34135. PMID 9012790.
- Thoms S, Erdmann R (October 2005). "Dynamin-related proteins and Pex11 proteins in peroxisome division and proliferation". The FEBS Journal. 272 (20): 5169â€“81. doi:10.1111/j.1742-4658.2005.04939.x. PMID 16218949.
- Hinshaw JE, Schmid SL (March 1995). "Dynamin self-assembles into rings suggesting a mechanism for coated vesicle budding". Nature. 374 (6518): 190â€“2. doi:10.1038/374190a0. PMID 7877694.
- Praefcke GJ, McMahon HT (February 2004). "The dynamin superfamily: universal membrane tubulation and fission molecules?". Nature Reviews. Molecular Cell Biology. 5 (2): 133â€“47. doi:10.1038/nrm1313. PMID 15040446. Lay summary – Dynamin Home Page.
- Sundborger AC, Fang S, Heymann JA, Ray P, Chappie JS, Hinshaw JE (August 2014). "A dynamin mutant defines a superconstricted prefission state". Cell Reports. 8 (3): 734â€“42. doi:10.1016/j.celrep.2014.06.054. PMC 4142656. PMID 25088425.
- Kong L, Sochacki KA, Wang H, Fang S, Canagarajah B, Kehr AD, Rice WJ, Strub MP, Taraska JW, Hinshaw JE (August 2018). "Cryo-EM of the dynamin polymer assembled on lipid membrane". Nature. 560 (7717): 258â€“262. doi:10.1038/s41586-018-0378-6. PMC 6121775. PMID 30069048.
- Mattila JP, Shnyrova AV, Sundborger AC, Hortelano ER, Fuhrmans M, Neumann S, MÃ¼ller M, Hinshaw JE, Schmid SL, Frolov VA (August 2015). "A hemi-fission intermediate links two mechanistically distinct stages of membrane fission". Nature. 524 (7563): 109â€“113. doi:10.1038/nature14509. PMC 4529379. PMID 26123023.
- Roux A, Uyhazi K, Frost A, De Camilli P (May 2006). "GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission". Nature. 441 (7092): 528â€“31. doi:10.1038/nature04718. PMID 16648839.
- ZÃ¼chner S, Noureddine M, Kennerson M, Verhoeven K, Claeys K, De Jonghe P, et al. (March 2005). "Mutations in the pleckstrin homology domain of dynamin 2 cause dominant intermediate Charcot-Marie-Tooth disease". Nature Genetics. 37 (3): 289â€“94. doi:10.1038/ng1514. PMID 15731758.
- Dhindsa RS, Bradrick SS, Yao X, Heinzen EL, Petrovski S, Krueger BJ, Johnson MR, Frankel WN, Petrou S, Boumil RM, Goldstein DB (June 2015). "Epileptic encephalopathy-causing mutations in DNM1 impair synaptic vesicle endocytosis". Neurology. Genetics. 1 (1): e4. doi:10.1212/01.NXG.0000464295.65736.da. PMID 27066543.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
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This tab holds annotation information from the InterPro database.
InterPro entry IPR000375Dynamin is a microtubule-associated force-producing protein of 100 Kd which is involved in the production of microtubule bundles. At the N terminus of dynamin is a GTPase domain (see INTERPRO), and at the C terminus is a PH domain (see INTERPRO). Between these two domains lies a central region of unknown function, which this entry represents.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||GTP binding (GO:0005525)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Pfam-B_220 (release 3.0)|
|Author:||Finn RD , Bateman A|
|Number in seed:||215|
|Number in full:||7631|
|Average length of the domain:||249.20 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||35.35 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||20|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There are 7 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Dynamin_M domain has been found. There are 134 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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