Summary: Dynein heavy chain region D6 P-loop domain
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Dynein Edit Wikipedia article
Dynein is a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work. Dynein transports various cellular cargos, provides forces and displacements important in mitosis, and drives the beat of eukaryotic cilia and flagella. All of these functions rely on dynein's ability to move towards the minus-end of the microtubules, known as retrograde transport, thus, they are called "minus-end directed motors". In contrast, kinesin motor proteins move toward the microtubules' plus end.
|Dynein heavy chain, N-terminal region 1|
|Dynein heavy chain, N-terminal region 2|
|Dynein heavy chain and region D6 of dynein motor|
|Dynein light intermediate chain (DLIC)|
|Dynein light chain type 1|
structure of the human pin/lc8 dimer with a bound peptide
Cytoplasmic dynein, found in all animal cells and possibly plant cells as well, performs functions necessary for cell survival such as organelle transport and centrosome assembly. Cytoplasmic dynein moves processively along the microtubule; that is, one or the other of its stalks is always attached to the microtubule so that the dynein can "walk" a considerable distance along a microtubule without detaching.
Cytoplasmic dynein helps to position the Golgi complex and other organelles in the cell. It also helps transport cargo needed for cell function such as vesicles made by the endoplasmic reticulum, endosomes, and lysosomes (Karp, 2005). Dynein is involved in the movement of chromosomes and positioning the mitotic spindles for cell division. Dynein carries organelles, vesicles and possibly microtubule fragments along the axons of neurons toward the cell body in a process called retrograde axoplasmic transport.
Mitotic spindle positioning
Cytoplasmic dynein positions the spindle at the site of cytokinesis by anchoring to the cell cortex and pulling on astral microtubules emanating from centrosome. Budding yeast have been a powerful model organism to study this process and has shown that dynein is targeted to plus ends of astral microtubules and delivered to the cell cortex via an offloading mechanism.
Each molecule of the dynein motor is a complex protein assembly composed of many smaller polypeptide subunits. Cytoplasmic and axonemal dynein contain some of the same components, but they also contain some unique subunits.
Cytoplasmic dynein, which has a molecular mass of about 1.5 megadaltons (MDa), is a dimer of dimers, containing approximately twelve polypeptide subunits: two identical "heavy chains", 520 kDa in mass, which contain the ATPase activity and are thus responsible for generating movement along the microtubule; two 74 kDa intermediate chains which are believed to anchor the dynein to its cargo; two 53–59 kDa light intermediate chains; and several light chains..
The force-generating ATPase activity of each dynein heavy chain is located in its large doughnut-shaped "head", which is related to other AAA proteins, while two projections from the head connect it to other cytoplasmic structures. One projection, the coiled-coil stalk, binds to and "walks" along the surface of the microtubule via a repeated cycle of detachment and reattachment. The other projection, the extended tail, binds to the light intermediate, intermediate and light chain subunits which attach dynein to its cargo. The alternating activity of the paired heavy chains in the complete cytoplasmic dynein motor enables a single dynein molecule to transport its cargo by "walking" a considerable distance along a microtubule without becoming completely detached.
Yeast dynein can walk along microtubules without detaching, however in metazoans, cytoplasmic dynein must be activated by the binding of dynactin, another multisubunit protein that is essential for mitosis, and a cargo adaptor. The tri-complex, which includes dynein, dynactin and a cargo adaptor, is ultra-processive and can walk long distances without detaching in order to reach the cargo's intracellular destination. Cargo adaptors identified thus far include BicD2, Hook3, FIP3 and Spindly. The light intermediate chain, which is a member of the Ras superfamily, mediates the attachment of several cargo adaptors to the dynein motor. The other tail subunits may also help facilitate this interaction as evidenced in a low resolution structure of dynein-dynactin-BicD2.
One major form of motor regulation within cells for dynein is dynactin. It may be required for almost all cytoplasmic dynein functions. Currently, it is the best studied dynein partner. Dynactin is a protein that aids in intracellular transport throughout the cell by linking to cytoplasmic dynein. Dynactin can function as a scaffold for other proteins to bind to. It also functions as a recruiting factor that localizes dynein to where it should be. There is also some evidence suggesting that it may regulate kinesin-2. The dynactin complex is composed of more than 20 subunits, of which p150(Glued) is the largest. There is no definitive evidence that dynactin by itself affects the velocity of the motor. It does, however, affect the processivity of the motor. The binding regulation is likely allosteric: experiments have shown that the enhancements provided in the processivity of the dynein motor do not depend on the p150 subunit binding domain to the microtubules.
Axonemal dyneins come in multiple forms that contain either one, two or three non-identical heavy chains (depending upon the organism and location in the cilium). Each heavy chain has a globular motor domain with a doughnut-shaped structure believed to resemble that of other AAA proteins, a coiled coil "stalk" that binds to the microtubule, and an extended tail (or "stem") that attaches to a neighboring microtubule of the same axoneme. Each dynein molecule thus forms a cross-bridge between two adjacent microtubules of the ciliary axoneme. During the "power stroke", which causes movement, the AAA ATPase motor domain undergoes a conformational change that causes the microtubule-binding stalk to pivot relative to the cargo-binding tail with the result that one microtubule slides relative to the other (Karp, 2005). This sliding produces the bending movement needed for cilia to beat and propel the cell or other particles. Groups of dynein molecules responsible for movement in opposite directions are probably activated and inactivated in a coordinated fashion so that the cilia or flagella can move back and forth. The radial spoke has been proposed as the (or one of the) structures that synchronizes this movement.
The regulation of axonemal dynein activity is critical for flagellar beat frequency and cilia waveform. Modes of axonemal dynein regulation include phosphorylation, redox, and calcium. Mechanical forces on the axoneme also affect anoxemal dynein function. The heavy chains of inner and outer arms of axonemal dynein are phosphorylated/dephosphorylated to control the rate of microtubule sliding. Thioredoxins associated with the other axonemal dynein arms are oxidized/reduced to regulate where dynein binds in the axoneme. Centerin and components of the outer axonemal dynein arms detect fluctuations in calcium concentration. Calcium fluctuations play an important role in altering cilia waveform and flagellar beat frequency (King, 2012).
The protein responsible for movement of cilia and flagella was first discovered and named dynein in 1963 (Karp, 2005). 20 years later, cytoplasmic dynein, which had been suspected to exist since the discovery of flagellar dynein, was isolated and identified (Karp, 2005).
Chromosome segregation during meiosis
Segregation of homologous chromosomes to opposite poles of the cell occurs during the first division of meiosis. Proper segregation is essential for producing haploid meiotic products with a normal complement of chromosomes. The formation of chiasmata (crossover recombination events) appears to generally facilitate proper segregation. However, in the fission yeast Schizosaccharomyces pombe, when chiasmata are absent, dynein promotes segregation. Dhc1, the motor subunit of dynein, is required for chromosomal segregation in both the presence and absence of chiasmata. The dynein light chain Dlc1 protein is also required for segregation, specifically when chiasmata are absent.
- Gerald Karp; Kurt Beginnen; Sebastian Vogel; Susanne Kuhlmann-Krieg (2005). Molekulare Zellbiologie (in French). Springer. ISBN 978-3-540-23857-7.
- Samora CP, Mogessie B, Conway L, Ross JL, Straube A, McAinsh AD (August 2011). "MAP4 and CLASP1 operate as a safety mechanism to maintain a stable spindle position in mitosis". Nature Cell Biology. 13 (9): 1040–50. doi:10.1038/ncb2297. PMID 21822276.
- Kiyomitsu T, Cheeseman IM (February 2012). "Chromosome- and spindle-pole-derived signals generate an intrinsic code for spindle position and orientation". Nature Cell Biology. 14 (3): 311–7. doi:10.1038/ncb2440. PMC . PMID 22327364.
- Eshel D, Urrestarazu LA, Vissers S, Jauniaux JC, van Vliet-Reedijk JC, Planta RJ, Gibbons IR (December 1993). "Cytoplasmic dynein is required for normal nuclear segregation in yeast". Proceedings of the National Academy of Sciences of the United States of America. 90 (23): 11172–6. doi:10.1073/pnas.90.23.11172. PMC . PMID 8248224.
- Li YY, Yeh E, Hays T, Bloom K (November 1993). "Disruption of mitotic spindle orientation in a yeast dynein mutant". Proceedings of the National Academy of Sciences of the United States of America. 90 (21): 10096–100. doi:10.1073/pnas.90.21.10096. PMC . PMID 8234262.
- Carminati JL, Stearns T (August 1997). "Microtubules orient the mitotic spindle in yeast through dynein-dependent interactions with the cell cortex". The Journal of Cell Biology. 138 (3): 629–41. doi:10.1083/jcb.138.3.629. PMC . PMID 9245791.
- Lee WL, Oberle JR, Cooper JA (February 2003). "The role of the lissencephaly protein Pac1 during nuclear migration in budding yeast". The Journal of Cell Biology. 160 (3): 355–64. doi:10.1083/jcb.200209022. PMC . PMID 12566428.
- Lee WL, Kaiser MA, Cooper JA (January 2005). "The offloading model for dynein function: differential function of motor subunits". The Journal of Cell Biology. 168 (2): 201–7. doi:10.1083/jcb.200407036. PMC . PMID 15642746.
- doi:10.1242/jcs.120725. PMID 23525020.; Carter AP (February 2013). "Crystal clear insights into how the dynein motor moves". Journal of Cell Science. 126 (Pt 3): 705–13.
- McKenney RJ, Huynh W, Tanenbaum ME, Bhabha G, Vale RD (July 2014). "Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes". Science. 345 (6194): 337–41. doi:10.1126/science.1254198. PMC . PMID 25035494.
- Schroeder CM, Ostrem JM, Hertz NT, Vale RD (October 2014). "A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region". eLife. 3: e03351. doi:10.7554/eLife.03351. PMC . PMID 25272277.
- Urnavicius L, Zhang K, Diamant AG, Motz C, Schlager MA, Yu M, Patel NA, Robinson CV, Carter AP (March 2015). "The structure of the dynactin complex and its interaction with dynein". Science. 347 (6229): 1441–6. doi:10.1126/science.aaa4080. PMC . PMID 25814576.
- Karki, Sher; Holzbaur, Erika LF (1999-02-01). "Cytoplasmic dynein and dynactin in cell division and intracellular transport". Current Opinion in Cell Biology. 11 (1): 45–53. doi:10.1016/S0955-0674(99)80006-4.
- Moughamian, Armen J.; Osborn, Gregory E.; Lazarus, Jacob E.; Maday, Sandra; Holzbaur, Erika L.F. (2013-08-07). "Ordered Recruitment of Dynactin to the Microtubule Plus-End is Required for Efficient Initiation of Retrograde Axonal Transport". The Journal of Neuroscience. 33 (32): 13190–13203. doi:10.1523/JNEUROSCI.0935-13.2013. ISSN 0270-6474. PMC . PMID 23926272.
- Moughamian, Armen J.; Holzbaur, Erika L. F. (2012-04-26). "Dynactin Is Required for Transport Initiation from the Distal Axon". Neuron. 74 (2): 331–343. doi:10.1016/j.neuron.2012.02.025. PMC . PMID 22542186.
- Berezuk, Matthew A.; Schroer, Trina A. (2007-02-01). "Dynactin enhances the processivity of kinesin-2". Traffic. 8 (2): 124–129. doi:10.1111/j.1600-0854.2006.00517.x. ISSN 1398-9219. PMID 17181772.
- Urnavicius, Linas; Zhang, Kai; Diamant, Aristides G.; Motz, Carina; Schlager, Max A.; Yu, Minmin; Patel, Nisha A.; Robinson, Carol V.; Carter, Andrew P. (2015-03-27). "The structure of the dynactin complex and its interaction with dynein". Science. 347 (6229): 1441–1446. doi:10.1126/science.aaa4080. ISSN 0036-8075. PMC . PMID 25814576.
- Schroer, Trina A. (2004-10-08). "DYNACTIN". https://dx.doi.org/10.1146/annurev.cellbio.20.012103.094623. doi:10.1146/annurev.cellbio.20.012103.094623. Retrieved 2017-05-14. External link in
- King, S. J.; Schroer, T. A. (2000-01-01). "Dynactin increases the processivity of the cytoplasmic dynein motor". Nature Cell Biology. 2 (1): 20–24. doi:10.1038/71338. ISSN 1465-7392. PMID 10620802.
- Kardon, Julia R.; Reck-Peterson, Samara L.; Vale, Ronald D. (2009-04-07). "Regulation of the processivity and intracellular localization of Saccharomyces cerevisiae dynein by dynactin". Proceedings of the National Academy of Sciences of the United States of America. 106 (14): 5669–5674. doi:10.1073/pnas.0900976106. ISSN 1091-6490. PMC . PMID 19293377.
- King, Stephen M. (2017-05-08). "Integrated Control of Axonemal Dynein AAA+ Motors". 179 (2): 222–228. doi:10.1016/j.jsb.2012.02.013. ISSN 1047-8477. PMC . PMID 22406539.
- Davis L, Smith GR (June 2005). "Dynein promotes achiasmate segregation in Schizosaccharomyces pombe". Genetics. 170 (2): 581–90. doi:10.1534/genetics.104.040253. PMC . PMID 15802518.
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.
Dynein heavy chain region D6 P-loop domain Provide feedback
This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains . The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained .
Internal database links
|SCOOP:||AAA_16 AAA_3 AAA_5 AAA_lid_11|
|Similarity to PfamA using HHSearch:||AAA_9|
This tab holds annotation information from the InterPro database.
InterPro entry IPR004273
Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules.
Dynein is composed of a number of ATP-binding large subunits, intermediate size subunits and small subunits (see INTERPRO). This family represents the C-terminal region of dynein heavy chain. The dynein heavy chain also exhibits ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||dynein complex (GO:0030286)|
|Molecular function||microtubule motor activity (GO:0003777)|
|Biological process||microtubule-based movement (GO:0007018)|
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AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes .
The clan contains the following 229 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_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulphotransf SWI2_SNF2 T2SSE 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 TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE Zeta_toxin Zot
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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_928 (release 6.4)|
|Author:||Griffiths-Jones SR , Bateman A|
|Number in seed:||478|
|Number in full:||5823|
|Average length of the domain:||119.30 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||3.32 %|
|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:||15|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
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.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
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.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 4 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 Dynein_heavy domain has been found. There are 23 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.
Loading structure mapping...