Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
75  structures 537  species 5  interactions 2008  sequences 30  architectures

Family: Dynein_light (PF01221)

Summary: Dynein light chain type 1

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Dynein Edit Wikipedia article

Cytoplasmic dynein on a microtubule
Cytoplasmic dynein has two heavy chains with globular "heads" that "walk" along the microtubule, to which they are bound by the "stalks". Dynactin (not shown) may help attach the light chains to the cargo. Interactions between the "stalks" and the microtubule must repeatedly form and break (see main text for details)

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.

Classification

Dynein heavy chain, N-terminal region 1
Identifiers
Symbol DHC_N1
Pfam PF08385
InterPro IPR013594
Dynein heavy chain, N-terminal region 2
Identifiers
Symbol DHC_N2
Pfam PF08393
InterPro IPR013602
Dynein heavy chain and region D6 of dynein motor
Identifiers
Symbol Dynein_heavy
Pfam PF03028
InterPro IPR004273
Dynein light intermediate chain (DLIC)
Identifiers
Symbol DLIC
Pfam PF05783
Pfam clan CL0023
Dynein light chain type 1
PDB 1cmi EBI.jpg
structure of the human pin/lc8 dimer with a bound peptide
Identifiers
Symbol Dynein_light
Pfam PF01221
InterPro IPR001372
PROSITE PDOC00953
SCOP 1bkq
SUPERFAMILY 1bkq

Dyneins can be divided into two groups: cytoplasmic dyneins and axonemal dyneins, which are also called ciliary or flagellar dyneins.

Function

Axonemal dynein causes sliding of microtubules in the axonemes of cilia and flagella and is found only in cells that have those structures.

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.[1] 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.[1] 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.[2][3] Dynein carries organelles, vesicles and possibly microtubule fragments along the axons of neurons toward the cell body in a process called retrograde axoplasmic transport.[1]

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.[4][5][6] 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.[7][8]

Structure

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

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.[9] 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, FIP3and Spindly.[9] The light intermediate chain, which is a member of the Ras superfamily, mediates the attachment of several cargo adaptors to the dynein motor.[10] The other tail subunits may also help facilitate this interaction as evidenced in a low resolution structure of dynein-dynactin-BicD2.[11]

Axonemal dynein

A cross-section of an axoneme, with axonemal dynein arms

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.

History

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.[12] Dhc1, the motor subunit of dynein, is required for chromosomal segregation in both the presence and absence of chiasmata.[12] The dynein light chain Dlc1 protein is also required for segregation, specifically when chiasmata are absent.

See also

References

  1. ^ a b c Gerald Karp; Kurt Beginnen; Sebastian Vogel; Susanne Kuhlmann-Krieg (2005). Molekulare Zellbiologie (in French). Springer. ISBN 978-3-540-23857-7. 
  2. ^ Samora, CP; Mogessie, B; Conway, L; Ross, JL; Straube, A; McAinsh, AD (Aug 7, 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. 
  3. ^ Kiyomitsu, Tomomi; Iain M. Cheeseman (2012-02-12). "Chromosome- and spindle-pole-derived signals generate an intrinsic code for spindle position and orientation". Nature Cell Biology. doi:10.1038/ncb2440. ISSN 1465-7392. Retrieved 2012-02-14. 
  4. ^ Eshel, D.; Urrestarazu, L. A.; Vissers, S.; Jauniaux, J. C.; van Vliet-Reedijk, J. C.; Planta, R. J.; Gibbons, I. R. (1993-12-01). "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): 11172–11176. doi:10.1073/pnas.90.23.11172. ISSN 0027-8424. PMC 47944Freely accessible. PMID 8248224. 
  5. ^ Li, Y. Y.; Yeh, E.; Hays, T.; Bloom, K. (1993-11-01). "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): 10096–10100. doi:10.1073/pnas.90.21.10096. ISSN 0027-8424. PMC 47720Freely accessible. PMID 8234262. 
  6. ^ Carminati, J. L.; Stearns, T. (1997-08-11). "Microtubules orient the mitotic spindle in yeast through dynein-dependent interactions with the cell cortex". The Journal of Cell Biology. 138 (3): 629–641. doi:10.1083/jcb.138.3.629. ISSN 0021-9525. PMC 2141630Freely accessible. PMID 9245791. 
  7. ^ Lee, Wei-Lih; Oberle, Jessica R.; Cooper, John A. (2003-02-03). "The role of the lissencephaly protein Pac1 during nuclear migration in budding yeast". The Journal of Cell Biology. 160 (3): 355–364. doi:10.1083/jcb.200209022. ISSN 0021-9525. PMC 2172672Freely accessible. PMID 12566428. 
  8. ^ Lee, Wei-Lih; Kaiser, Michelle A.; Cooper, John A. (2005-01-17). "The offloading model for dynein function: differential function of motor subunits". The Journal of Cell Biology. 168 (2): 201–207. doi:10.1083/jcb.200407036. ISSN 0021-9525. PMC 2171595Freely accessible. PMID 15642746. 
  9. ^ a b McKenney, Richard J.; Huynh, Walter; Tanenbaum, Marvin E.; Bhabha, Gira; Vale, Ronald D. (2014-07-18). "Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes". Science. 345 (6194): 337–341. doi:10.1126/science.1254198. ISSN 0036-8075. PMC 4224444Freely accessible. PMID 25035494. 
  10. ^ Schroeder, Courtney M.; Ostrem, Jonathan ML; Hertz, Nicholas T.; Vale, Ronald D. (2014-10-01). "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. ISSN 2050-084X. PMC 4359372Freely accessible. PMID 25272277. 
  11. ^ 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 4413427Freely accessible. PMID 25814576. 
  12. ^ a b Davis L, Smith GR (2005). "Dynein promotes achiasmate segregation in Schizosaccharomyces pombe". Genetics. 170 (2): 581–90. doi:10.1534/genetics.104.040253. PMC 1450395Freely accessible. PMID 15802518. 

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.

Dynein light chain type 1 Provide feedback

No Pfam abstract.

Literature references

  1. Tochio H, Ohki S, Zhang Q, Li M, Zhang M; , Nat Struct Biol 1998;5:965-969.: Solution structure of a protein inhibitor of neuronal nitric oxide synthase. PUBMED:9808041 EPMC:9808041


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001372

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 (see INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [PUBMED:7744782, PUBMED:8628263].

Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [PUBMED:10426949, PUBMED:14561217].

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...

Loading domain graphics...

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(337)
Full
(2008)
Representative proteomes UniProt
(3643)
NCBI
(3002)
Meta
(9)
RP15
(761)
RP35
(1433)
RP55
(1932)
RP75
(2221)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(337)
Full
(2008)
Representative proteomes UniProt
(3643)
NCBI
(3002)
Meta
(9)
RP15
(761)
RP35
(1433)
RP55
(1932)
RP75
(2221)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(337)
Full
(2008)
Representative proteomes UniProt
(3643)
NCBI
(3002)
Meta
(9)
RP15
(761)
RP35
(1433)
RP55
(1932)
RP75
(2221)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: none
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 337
Number in full: 2008
Average length of the domain: 82.60 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 64.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.9 24.9
Trusted cut-off 25.1 24.9
Noise cut-off 24.8 24.7
Model length: 86
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

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.

Interactions

There are 5 interactions for this family. More...

Dynein_light Dynein_IC2 bZIP_1 Tctex-1 Dynein_IC2

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 Dynein_light domain has been found. There are 75 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.

Loading structure mapping...