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134  structures 1099  species 7  interactions 7631  sequences 153  architectures

Family: Dynamin_M (PF01031)

Summary: Dynamin central region

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This is the Wikipedia entry entitled "Dynamin". More...

Dynamin Edit Wikipedia article

Dynamin family
PDB 2aka EBI.jpg
Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin I from Rattus norvegicus
Identifiers
SymbolDynamin_N
PfamPF00350
Pfam clanCL0023
InterProIPR001401
PROSITEPDOC00362
Dynamin central region
PDB 2aka EBI.jpg
Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin I from Rattus norvegicus
Identifiers
SymbolDynamin_M
PfamPF01031
InterProIPR000375

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.[1][2][3] Dynamin family members also play a role in many processes including division of organelles,[4] cytokinesis and microbial pathogen resistance.

Structure

Dynamin assembled into helical polymers as visualized by negative stain electron microscopy.[5]

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.[3][6] 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.

Function

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.[7][8] 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.[8] Constriction around the vesicle neck leads to the formation of a hemi-fission membrane state that ultimately results in membrane scission.[2][6][9] 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.[10]

Types

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:

Disease implications

Mutations in Dynamin II have been found to cause dominant intermediate Charcot-Marie-Tooth disease.[11] Epileptic encephalopathy–causing de novo mutations in dynamin have been suggested to cause dysfunction of vesicle scission during synaptic vesicle endocytosis.[12]

References

  1. ^ a b Henley JR, Cao H, McNiven MA (December 1999). "Participation of dynamin in the biogenesis of cytoplasmic vesicles". FASEB Journal. 13 Suppl 2 (9002): S243–7. doi:10.1096/fasebj.13.9002.S243. PMID 10619136.
  2. ^ a b 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.
  3. ^ a b 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): 377–84. doi:10.1073/pnas.94.2.377. PMC 34135. PMID 9012790.
  4. ^ Thoms S, Erdmann R (October 2005). "Dynamin-related proteins and Pex11 proteins in peroxisome division and proliferation". The FEBS Journal. 272 (20): 5169–81. doi:10.1111/j.1742-4658.2005.04939.x. PMID 16218949.
  5. ^ Hinshaw JE, Schmid SL (March 1995). "Dynamin self-assembles into rings suggesting a mechanism for coated vesicle budding". Nature. 374 (6518): 190–2. doi:10.1038/374190a0. PMID 7877694.
  6. ^ a b c Praefcke GJ, McMahon HT (February 2004). "The dynamin superfamily: universal membrane tubulation and fission molecules?". Nature Reviews. Molecular Cell Biology. 5 (2): 133–47. doi:10.1038/nrm1313. PMID 15040446. Lay summary – Dynamin Home Page.
  7. ^ 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): 734–42. doi:10.1016/j.celrep.2014.06.054. PMC 4142656. PMID 25088425.
  8. ^ a b 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): 258–262. doi:10.1038/s41586-018-0378-6. PMC 6121775. PMID 30069048.
  9. ^ Mattila JP, Shnyrova AV, Sundborger AC, Hortelano ER, Fuhrmans M, Neumann S, Müller M, Hinshaw JE, Schmid SL, Frolov VA (August 2015). "A hemi-fission intermediate links two mechanistically distinct stages of membrane fission". Nature. 524 (7563): 109–113. doi:10.1038/nature14509. PMC 4529379. PMID 26123023.
  10. ^ 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): 528–31. doi:10.1038/nature04718. PMID 16648839.
  11. ^ Züchner 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): 289–94. doi:10.1038/ng1514. PMID 15731758.
  12. ^ 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.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Dynamin central region Provide feedback

This region lies between the GTPase domain, see PF00350 and the pleckstrin homology (PH) domain, see PF00169.

This tab holds annotation information from the InterPro database.

InterPro entry IPR000375

Dynamin 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.

Gene Ontology

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Domain organisation

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Alignments

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(215)
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(11317)
NCBI
(16316)
Meta
(39)
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(1763)
RP35
(3979)
RP55
(5595)
RP75
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  Seed
(215)
Full
(7631)
Representative proteomes UniProt
(11317)
NCBI
(16316)
Meta
(39)
RP15
(1763)
RP35
(3979)
RP55
(5595)
RP75
(6990)
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  Seed
(215)
Full
(7631)
Representative proteomes UniProt
(11317)
NCBI
(16316)
Meta
(39)
RP15
(1763)
RP35
(3979)
RP55
(5595)
RP75
(6990)
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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_220 (release 3.0)
Previous IDs: dynamin_2;
Type: Family
Sequence Ontology: SO:0100021
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.5 28.5
Trusted cut-off 28.5 28.5
Noise cut-off 28.3 28.4
Model length: 285
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 7 interactions for this family. More...

GED Dynamin_M Dynamin_N Dynamin_N PH Myosin_head GED

Structures

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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