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32  structures 1940  species 2  interactions 6429  sequences 111  architectures

Family: Dynamin_N (PF00350)

Summary: Dynamin family

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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
Symbol Dynamin_N
Pfam PF00350
Pfam clan CL0023
InterPro IPR001401
PROSITE PDOC00362
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
Symbol Dynamin_M
Pfam PF01031
InterPro IPR000375

Dynamin is a GTPase responsible for endocytosis in the eukaryotic cell. Dynamins 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 also plays a role in many processes including division of organelles,[4] cytokinesis and microbial pathogen resistance.

Dynamin is part of the "dynamin superfamily," which includes classical dynamins, dynamin-like proteins, Mx proteins, OPA, mitofusins, and GBPs. 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][5]

Function[edit]

As a vesicle invaginates, dynamin forms a spiral around the neck of the vesicle. Once the spiral is in place, it extends lengthwise and constricts through GTP hydrolysis. This lengthening and tightening of the coil around the vesicle neck causes it to break and results in the pinching off of the vesicle from the parent membrane. An example of a vesicle is a clathrin-coated pit.[2][5]

To view a ‘cartoon’ image of the non-constricted and constricted state of dynamin spirals, please follow this link: http://dynamin.niddk.nih.gov/figure5.html.[2] The first structure on the left is dynamin in its relaxed state. The structure on the right is dynamin in its constricted state. This shows the extent to which dynamin tightens and changes when GTP is converted to GDP.[1]

This constriction is in part the result of the twisting activity of dynamin [6] This twisting required GTP hydrolysis. Dynamin is the only molecular motor known to have a twisting activity. Dynamin is a right-handed helix and has a right-handed twisting activity that explains its tightening and the reduction in the pitch of the helix described above.

Types[edit]

In mammals, three different dynamin genes have been identified:

Disease implications[edit]

Mutations in Dynamin II have been found to cause dominant intermediate Charcot-Marie-Tooth disease.[7]

References[edit]

  1. ^ a b c Henley, J.R., Cao, H., McNicven, M.A. (1999). “Participation of dynamin in the biogenesis of cytoplasmic vesicles”. The FASEB Journal, 13, S243-S247.
  2. ^ a b c 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, J.R.; Cook, T.; McNiven, M.A. (1997). "The dynamins: Redundant or distinct functions for an expanding family of related GTPases?". Proc. Natl Acad. Sci. USA 94 (2): 377–384. doi:10.1073/pnas.94.2.377. 
  4. ^ Thoms S, Erdmann R (Oct 2005). "Dynamin-related proteins and Pex11 proteins in peroxisome division and proliferation.". FEBS J 272 (20): 5169–81. doi:10.1111/j.1742-4658.2005.04939.x. PMID 16218949. 
  5. ^ a b c McMahon. (2004). “Researching Endocytic Mechanisms: Dynamin. Accompaniment to Nature Reviews Molecular Cell Biology, 5, 133-147.
  6. ^ Roux, A; Uyhazi, K; Frost, A; De Camilli, P (2006-04-30). "GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission". Nature 441 (7092): 528–31. doi:10.1038/nature04718. PMID 16648839. 
  7. ^ Stephan Zuchner, Maher Noureddine, Marina Kennerson, Kristien Verhoeven, Kristl Claeys, Peter De Jonghe, John Merory, Sofia A. Oliveira, Marcy C. Speer, Judith E. Stenger, Gina Walizada, Danqing Zhu, Margaret A. Pericak-Vance, Garth Nicholson, Vincent Timmerman & Jeffery M. Vance (March 2005). "Mutations in the pleckstrin homology domain of dynamin 2 cause dominant intermediate Charcot-Marie-Tooth disease". Nature Genetics 37 (3): 289–294. doi:10.1038/ng1514. PMID 15731758. 

External links[edit]

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.

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Literature references

  1. Warnock DE, Schmid SL; , Bioessays 1996;18:885-893.: Dynamin GTPase, a force-generating molecular switch. PUBMED:8939066 EPMC:8939066

  2. Obar RA, Collins CA, Hammarback JA, Shpetner HS, Vallee RB; , Nature 1990;347:256-261.: Molecular cloning of the microtubule-associated mechanochemical enzyme dynamin reveals homology with a new family of GTP-binding proteins. PUBMED:2144893 EPMC:2144893


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001401

Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another. Dynamins are large GTPases that belong to a protein superfamily [PUBMED:15040446] that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins [PUBMED:2142876, PUBMED:2112425, PUBMED:1532158, PUBMED:2607176], and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance.

The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity.

This entry represents the GTPase domain, containing the GTP-binding motifs that are needed for guanine-nucleotide binding and hydrolysis. The conservation of these motifs is absolute except for the the final motif in guanylate-binding proteins. The GTPase catalytic activity can be stimulated by oligomerisation of the protein, which is mediated by interactions between the GTPase domain, the middle domain and the GED.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 198 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_4 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_2 Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arch_ATPase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 Bac_DnaA CbiA CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1253 DUF1611 DUF2075 DUF2478 DUF258 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GTP_EFTU GTP_EFTU_D2 GTP_EFTU_D4 Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK IIGP IPPT IPT IstB_IS21 KaiC KAP_NTPase Kinesin Kinesin-relat_1 Kinesin-related KTI12 LpxK MCM MEDS Mg_chelatase Mg_chelatase_2 MipZ Miro MMR_HSR1 MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6 Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind UPF0079 UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YhjQ Zeta_toxin Zot

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(79)
Full
(6429)
Representative proteomes NCBI
(11019)
Meta
(2690)
RP15
(828)
RP35
(1542)
RP55
(2205)
RP75
(2723)
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  Seed
(79)
Full
(6429)
Representative proteomes NCBI
(11019)
Meta
(2690)
RP15
(828)
RP35
(1542)
RP55
(2205)
RP75
(2723)
Alignment:
Format:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(79)
Full
(6429)
Representative proteomes NCBI
(11019)
Meta
(2690)
RP15
(828)
RP35
(1542)
RP55
(2205)
RP75
(2723)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: dynamin;
Type: Family
Author: Finn RD
Number in seed: 79
Number in full: 6429
Average length of the domain: 176.80 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 26.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 168
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Dynamin_N Myosin_head

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_N domain has been found. There are 32 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 seqence.

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