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10  structures 88  species 0  interactions 96  sequences 2  architectures

Family: ANAPC16 (PF17256)

Summary: Anaphase Promoting Complex Subunit 16

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 "Anaphase-promoting complex". More...

Anaphase-promoting complex Edit Wikipedia article

Anaphase-promoting complex (also called the cyclosome or APC/C) is an E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome. The APC/C is a large complex of 11–13 subunit proteins, including a cullin (Apc2) and RING (Apc11) subunit much like SCF. Other parts of the APC/C still have unknown functions, but are highly conserved.[1]

It was the discovery of the APC/C (and SCF) and their key role in eukaryotic cell reproduction that established once and for all the importance of ubiquitin-mediated proteolysis in eukaryotic cell biology. Once perceived as a system exclusively involved in removing damaged protein from the cell, ubiquitination and subsequent protein degradation by the proteasome is now perceived as a universal regulatory mechanism for signal transduction whose importance approaches that of protein phosphorylation.

In 2014, the APC/C was mapped in 3D at a resolution of less than a nanometre, which also uncovered its secondary structure. Researchers have claimed this finding could transform the understanding of cancer and reveal new binding sites for future cancer drugs.[2][3]

Function

The APC/C's main function is to trigger the transition from metaphase to anaphase by tagging specific proteins for degradation. The three major targets for degradation by the APC/C are securin and S and M cyclins. Securin releases separase (a protease) after being degraded. The separase triggers the cleavage of cohesin, the protein complex that binds sister chromatids together. During metaphase, sister chromatids are linked by intact cohesin complexes. When securin undergoes ubiquitination by the APC/C and releases separase, which degrades cohesin, sister chromatids become free to move to opposite poles for anaphase. The APC/C also targets the mitotic cyclins for degradation, resulting in the inactivation of M-CDK (mitotic cyclin-dependent kinase) complexes, promoting exit from mitosis and cytokinesis.[1]

Unlike the SCF, activator subunits control the APC/C. Cdc20 and Cdh1 are the two activators of particular importance to the cell cycle. These proteins target the APC/C to specific sets of substrates at different times in the cell cycle, thus driving it forward. The APC/C also plays an integral role in maintenance of chromatin metabolism, particularly in G1 and G0, and plays a key role in phosphorylation of H3 through destruction of the aurora A kinase.[4]

The critical substrates of the APC/C appear to be securin and the B type cyclins. This is conserved between mammals and yeast. In fact, yeast are viable in the absence of the APC/C if the requirement for targeting these two substrates is eliminated.[5]

Subunits

The catalytic core of the APC/C consists of the cullin subunit Apc2 and RING H2 domain subunit Apc11. These two subunits catalyze ubiquitination of substrates when the C-terminal domain of Apc2 forms a tight complex with Apc11. In addition to the catalytic subunits, other core proteins of the APC are composed multiple repeat motifs with the main purpose of providing molecular scaffold support. These include Apc1, the largest subunit which contains 11 tandem repeats of 35–40 amino acid sequences, and Apc2, which contains three cullin repeats of approximately 130 amino acids total.[6]

Most notably, 4 subunits of yeast APC/C consist almost entirely of multiple repeats of the 34 amino acid tetratricopeptide residue (TPR) motif. These TPR subunits, Cdc16, Cdc27, Cdc23, and Apc5, mainly provide scaffolding and support to mediate other protein-protein interactions. Cdc27 and Cdc23 have been shown to support the binding of Cdc20 and Cdh1, as mutations in key residues of these subunits led to increased dissociation of the activators. Apc10/Doc1, has been shown to promote substrate binding by mediating their interactions with Cdh1 and Cdc20.[7]

The subunit Apc15 plays an important role in APC/CCdc20 activation following the bi-orientation of sister chromatids across the metaphase plate. When kinetochores are unattached to spindles, mitotic checkpoint complexes (MCC) and inhibit APC. In the absence of Apc15, MCCs and Cdc20 remain locked on the APC/C preventing its activity once the spindle checkpoint requirements are met. Apc15 mediates the turnover of Cdc20 and MCCs to provide information on the attachment state of kinetochores.[8]

Substrate recognition

APC/C substrates have recognition amino acid sequences that enable the APC/C to identify them. The most common sequence is known as the destruction box or D-box. APC/C brings together an E2 ubiquitin-conjugating enzyme and the D-box rather than being an intermediate covalent carrier.[9] The D-box should have a version of the following amino acid sequence: RXXLXXXXN, where R is arginine, X is any amino acid, L is Leucine, and N is asparagine. The Ken-box is another motif of importance. Its sequence should resemble the one that follows: KENXXXN, where K is lysine and E is glutamate. The last amino acid position in the Ken-box is highly variable. Though it has been shown that mutations in the sequences do inhibit destruction of the proteins "in vivo", there is still much to learn about how proteins are targeted by the APC/C.[1]

Once bound to APC/C, Cdc20 and Cdh1 serve as D and KEN box receptors for various APC substrates. Kraft et al. have shown that the substrates’ D boxes bind directly to the highly conserved WD40 repeat propeller region on the APC activators. It is important to note that the conserved area of the propeller of Cdh1 is much larger than that of Cdc20, allowing Cdh1 to have a broader substrate specificity, consistent with the fact that APC/CCdh1 also activates APC-mediated destruction of KEN box containing substrates. The D box further enhances protein degradation, for Lysine residues in close proximity to the D box serve as targets of ubiquitylation. It has been found that a Lys residue immediately C-terminal to the D box can function as a ubiquitin acceptor.[10]

Many APC substrates contain both D and KEN boxes, with their ubiquitylation by either APC/CCdc20 or APC/CCdh1 dependent on both sequences, yet some substrates contain only either a D box or a KEN box, in one or multiple copies. Having two distinct degradation sequences creates a high level of substrate specificity on the APC/C, with APC/CCdc20 being more dependent on the D box and APC/CCdh1 more dependent on the KEN box. For example, APC/CCdh1 is capable of ubiquitylating KEN box-only-containing substrates like Tome-1 and Sororin.[6]

Although Cdc20 and Cdh1 may serve as D and KEN box receptors, the low affinity of these co-activator–substrate interactions suggests that it is unlikely that the co-activators alone are sufficient to confer high-affinity substrate binding to the APC/CCdc20 and APC/CCdh1.[6] Consequently, core APC/C subunits, like Apc10, contribute towards substrate association as well. In APC/C constructs lacking the Apc10/Doc1 subunit, substrates like Clb2 are unable to associate with APCΔdoc1–Cdh1, while addition of purified Doc1 to the APCΔdoc1–Cdh1 construct restores the substrate binding ability.[7]

Metaphase to anaphase transition

As metaphase begins, the spindle checkpoint inhibits the APC/C until all sister-kinetochores are attached to opposite poles of the mitotic spindle, a process known as chromosome biorientation. When all kinetochores are properly attached, the spindle checkpoint is silenced and the APC/C can become active. M-Cdks phosphorylate subunits on the APC/C that promote binding to Cdc20. Securin and M cyclins (cyclin A and cyclin B) are then targeted by APC/CCdc20 for degradation. Once degraded, separin is released, cohesin is degraded and sister chromatids are prepared to move to their respective poles for anaphase.[1]

It is likely that, in animal cells, at least some of the activation of APC/CCdc20 occurs early in the cell cycle (prophase or prometaphase) based on the timing of the degradation of its substrates. Cyclin A is degraded early in mitosis, supporting the theory, but cyclin B and securin are not degraded until metaphase. The molecular basis of the delay is unknown, but is believed to involve the key to the correct timing of anaphase initiation. In animal cells the spindle checkpoint system contributes to the delay if it needs to correct the bi-orientation of chromosomes. Though how the spindle checkpoint system inhibits cyclin B and securin destruction while allowing cyclin A to be degraded is unknown. The delay may also be explained by unknown interactions with regulators, localization and phosphorylation changes.[1]

This initiates a negative feedback loop. While activation of APC/CCdc20 requires M-Cdk, the complex is also responsible for breaking the cyclin to deactivate M-CdK. This means that APC/CCdc20 fosters its own deactivation. It is possible that this negative feedback is the backbone of Cdk activity controlled by M and S cyclin concentration oscillations.[1]

M to G1 transition

Upon completion of mitosis, it is important that cells (except for embryonic ones) go through a growth period, known as G1 phase, to grow and produce factors necessary for the next cell cycle. Entry into another round of mitosis is prevented by inhibiting Cdk activity. While different processes are responsible for this inhibition, an important one is activation of the APC/C by Cdh1. This continued activation prevents the accumulation of cyclin that would trigger another round of mitosis and instead drives exit from mitosis.[1]

In the beginning of the cell cycle Cdh1 is phosphorylated by M-Cdk, preventing it from attaching to APC/C. APC/C is then free to attach to Cdc20 and usher the transition from metaphase to anaphase. As M-Cdk gets degraded later in mitosis, Cdc20 gets released and Cdh1 can bind to APC/C, keeping it activated through the M/G1 transition. A key difference to note is that while binding of Cdc20 to APC/C is dependent on phosphorylation of APC/C by mitotic Cdks, binding of Cdh1 is not. Thus, as APCCdc20 becomes inactivated during metaphase due to dephosphorylation resulting from inactive mitotic Cdks, Cdh1 is able to immediately bind to APC/C, taking Cdc20's place. Cdc20 is also a target of APC/CCdh1, ensuring that APC/CCdc20 is shut down. APC/CCdh1 then continues working in G1 to tag S and M cyclins for destruction. However, G1/S cyclins are not substrates of APC/CCdh1 and therefore accumulate throughout this phase and phosphorylate Cdh1. By late G1, enough of the G1/S cyclins have accumulated and phosphorylated Cdh1 to inactivate the APC/C until the next metaphase.[1]

Once in G1, APCCdh1 is responsible for the degradation various proteins that promote proper cell cycle progression. Geminin is a protein that binds to Cdt1 which prevents its binding to the origin recognition complex (ORC). APCCdh1 targets geminin for ubiquitination throughout G1, keeping its levels low. This allows Cdt1 to carry out its function during pre-RC assembly. When APCCdh1 becomes inactive due to phosphorylation of Cdh1 by G1/S cyclins, geminin activity is increased again. Additionally, Dbf4 stimulates Cell division cycle 7-related protein kinase (Cdc7) activity, which promotes activation of replication origins. APCCdh1 is thought to target Dbf4 for destruction. This could provide an answer as to how Cdc7 is activated at the beginning of a new cell cycle. Its activity likely corresponds to the inactivation of APC/CCdh1 by G/S cyclins.[1]

Additional regulation

APC/CCdc20 inactivation during early stages of the cell cycle is partially achieved by the protein Emi1. Initial experiments have shown that addition of Emi1 to Xenopus cycling extracts can prevent the destruction of endogenous cyclin A, cyclin B, and mitotic exit, suggesting that Emi1 is able to counteract the activity of the APC. Furthermore, depletion of Emi1 in somatic cells leads to the lack of accumulation of cyclin B. The lack of Emi1 likely leads to a lack of inhibition of the APC preventing cyclin B from accumulating.[11]

From these early observations, it has been confirmed that in G2 and early mitosis, Emi1 binds and inhibits Cdc20 by preventing its association with APC substrates. Cdc20 can still be phosphorylated and bind to APC/C, but bound Emi1 blocks Cdc20’s interaction with APC targets.[1] Emi1 association with Cdc20 allows for the stabilization of various cyclins throughout S and G2 phase, but Emi1's removal is essential for progression through mitosis. Thus, in late prophase, Emi1 is phosphorylated by Polo-like kinase, Plk. Plk is activated during early mitosis by Cdk1 activity, and its phosphorylation of Emi1’s BTRC (gene) βTrCP binding site makes it a target for SCF, leading to its subsequent destruction in prometaphase.[12] Emi1's destruction leads APC/CCdc20 activation, allowing for the destruction of cyclin A in early mitosis. Emi1 levels begin to rise again in G, which help inhibit APC/CCdh1.[1]

Regulation of APC/CCdc20 activity towards metaphase substrates like securin and cyclin B may be a result of intracellular localization. It is hypothesized that spindle checkpoint proteins that inhibit APC/CCdc20 only associate with a subset of the Cdc20 population localized near the mitotic spindle. In this manner, cyclin A can be degraded while cyclin B and securin are degraded only once sister chromatids have achieved bi-orientation.[1]

References

  1. ^ a b c d e f g h i j k l Morgan, David O. (2007). The Cell Cycle: Principles of Control. London: New Science Press. ISBN 0-9539181-2-2. 
  2. ^ "Scientists map one of most important proteins in life – and cancer". The Institute of Cancer Research. 20 July 2014. Retrieved 22 July 2014. 
  3. ^ "Molecular architecture and mechanism of the anaphase-promoting complex". Nature. 20 July 2014. Retrieved 22 July 2014. 
  4. ^ Bruce Alberts; Alexander Johnson; Julian Lewis; Martin Raff; Keith Roberts; Peter Walter, eds. (2002). "Chapter 17. The Cell Cycle and Programmed Cell Death". Molecular Biology of the Cell (4th ed.). Garland Science. ISBN 0-8153-3218-1. 
  5. ^ Thornton, Brian; Toczyski, David P. (2003). "Securin and B-cyclin/CDK are the only essential targets of the APC.". Nature Cell Biology. 5: 1090–1094. doi:10.1038/ncb1066. PMID 14634663. 
  6. ^ a b c Barford, David (2011). "Structural insights into anaphase-promoting complex function and mechanism". Philosophical Transactions of the Royal Society B: Biological Sciences. 366 (1584): 3605–3624. doi:10.1098/rstb.2011.0069. 
  7. ^ a b Passmore, Lori A.; McCormack, Elizabeth A.; Au, Shannon W.N.; Paul, Angela; Willison, Keith R.; Harper, J. Wade; Barford, David (2003). "Doc1 mediates the activity of the anaphase-promoting complex by contributing to substrate recognition". The EMBO Journal. 22 (4): 786–796. doi:10.1093/emboj/cdg084. PMC 145444Freely accessible. PMID 12574115. 
  8. ^ Mansfeld, Jorg; Collin, Philippe; Collins, Mark O.; Choudhary, Jyoti S.; Pines, Jonathon (2011). "APC15 drives the turnover of MCC-CDC20 to make the spindle assembly checkpoint responsive to kinetochore attachment". Nature Cell Biology. 13 (10): 1234–1243. doi:10.1038/ncb2347. PMC 3188299Freely accessible. PMID 21926987. 
  9. ^ King RW; Deshaies RJ; Peters JM; Kirschner MW. (1996). "How proteolysis drives the cell cycle". Science. 274 (5293): 1652–9. doi:10.1126/science.274.5293.1652. PMID 8939846. 
  10. ^ Kraft, Claudine; Vodermaier, Hartmut C.; Maurer-Stroh, Sebastian; Eisenhaber, Frank; Peters, Jan-Michael (2005). "The WD40 Propeller Domain of Cdh1 Functions as a Destruction Box Receptor for APC/C Substrates". Molecular Cell. 18 (5): 543–553. doi:10.1016/j.molcel.2005.04.023. PMID 15916961. 
  11. ^ JD, Reimann; Freed E; Hsu JY; Kramer ER; Peters JM; Jackson PK (2001). "Emi1 is a mitotic regulator that interacts with Cdc20 and inhibits the anaphase promoting complex". Cell. 105 (5): 645–655. doi:10.1016/S0092-8674(01)00361-0. PMID 11389834. 
  12. ^ Hansen, David; Alexander V. Loktev; Kenneth H. Ban; Peter K. Jackson. "Plk1 Regulates Activation of the Anaphase Promoting Complex by Phosphorylating and Triggering SCFβTrCP-dependent Destruction of the APC Inhibitor Emi1". Molecular Biology of the Cell. 15 (12): 5623–5634. doi:10.1091/mbc.E04-07-0598. PMC 532041Freely accessible. PMID 15469984. 

Further reading

External links

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

This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.[1]

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[2] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[3] This work showed that about two thirds of DUF families had a structure similar to a previously solved one and therefore likely to be divergent members of existing protein superfamilies, whereas about one third possessed a novel protein fold.

Frequency and conservation

Protein domains and DUFs in different domains of life. Left: Annotated domains. Right: domains of unknown function. Not all overlaps shown.[4]

More than 20% of all protein domains were annotated as DUFs in 2013. About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs.[4]

Role in biology

Many DUFs are highly conserved, indicating an important role in biology. However, many such DUFs are not essential, hence their biological role often remains unknown. For instance, DUF143 is present in most bacteria and eukaryotic genomes.[5] However, when it was deleted in Escherichia coli no obvious phenotype was detected. Later it was shown that the proteins that contain DUF143, are ribosomal silencing factors that block the assembly of the two ribosomal subunits.[5] While this function is not essential, it helps the cells to adapt to low nutrient conditions by shutting down protein biosynthesis. As a result, these proteins and the DUF only become relevant when the cells starve.[5] It is thus believed that many DUFs (or proteins of unknown function, PUFs) are only required under certain conditions.

Essential DUFs (eDUFs)

Goodacre et al. identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. These DUFs are called "essential DUFs" or eDUFs.[4]

External links

References

  1. ^ Bateman A, Coggill P, Finn RD (October 2010). "DUFs: families in search of function". Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (Pt 10): 1148–52. doi:10.1107/S1744309110001685. PMC 2954198Freely accessible. PMID 20944204. 
  2. ^ Schultz J, Milpetz F, Bork P, Ponting CP (May 1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. doi:10.1073/pnas.95.11.5857. PMC 34487Freely accessible. PMID 9600884. 
  3. ^ Jaroszewski L, Li Z, Krishna SS, et al. (September 2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874Freely accessible. PMID 19787035. 
  4. ^ a b c Goodacre, N. F.; Gerloff, D. L.; Uetz, P. (2013). "Protein Domains of Unknown Function Are Essential in Bacteria". MBio. 5 (1): e00744–e00713. doi:10.1128/mBio.00744-13. PMC 3884060Freely accessible. PMID 24381303. 
  5. ^ a b c Häuser, R.; Pech, M.; Kijek, J.; Yamamoto, H.; Titz, B. R.; Naeve, F.; Tovchigrechko, A.; Yamamoto, K.; Szaflarski, W.; Takeuchi, N.; Stellberger, T.; Diefenbacher, M. E.; Nierhaus, K. H.; Uetz, P. (2012). Hughes, Diarmaid, ed. "RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors". PLoS Genetics. 8 (7): e1002815. doi:10.1371/journal.pgen.1002815. PMC 3400551Freely accessible. PMID 22829778. 

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.

Anaphase Promoting Complex Subunit 16 Provide feedback

The Anaphase-promoting complex/cyclosome (APC/C) is a 1.5 megaDaltons assembly ubiquitin ligase complex comprising 19 subunits. This multifunctional ubiquitin-protein ligase targets different substrates for ubiquitylation and therefore regulates a variety of cellular processes such as cell division, differentiation, genome stability, energy metabolism, cell death, autophagy as well as carcinogenesis [1]. The APC/C complex contains two sub-complexes,the Platform and the Arc Lamp. The Arc Lamp, which mediates transient association with regulators and ubiquitination substrates, contains the small subunits APC16, CDC26, APC13, and tetratricopeptide repeat (TPR) proteins [2]. APC16 is a conserved subunit of the APC/C. APC16 was found in association with tandem-affinity-purified mitotic checkpoint complex protein complexes. APC16 is a bona fide subunit of human APC/C. It is present in APC/C complexes throughout the cell cycle. The phenotype of APC16-depleted cells copies depletion of other APC/C subunits, and APC16 is important for APC/C activity towards mitotic substrates. APC16 sequence homologues can be identified in metazoans, but not fungi, by four conserved primary sequence stretches [3].

Literature references

  1. Zhou Z, He M, Shah AA, Wan Y;, Cell Div. 2016;11:9.: Insights into APC/C: from cellular function to diseases and therapeutics. PUBMED:27418942 EPMC:27418942

  2. Yamaguchi M, Yu S, Qiao R, Weissmann F, Miller DJ, VanderLinden R, Brown NG, Frye JJ, Peters JM, Schulman BA;, J Mol Biol. 2015;427:1748-1764.: Structure of an APC3-APC16 complex: insights into assembly of the anaphase-promoting complex/cyclosome. PUBMED:25490258 EPMC:25490258

  3. Kops GJ, van der Voet M, Manak MS, van Osch MH, Naini SM, Brear A, McLeod IX, Hentschel DM, Yates JR 3rd, van den Heuvel S, Shah JV;, J Cell Sci. 2010;123:1623-1633.: APC16 is a conserved subunit of the anaphase-promoting complex/cyclosome. PUBMED:20392738 EPMC:20392738


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Domain organisation

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Curation and family details

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Curation View help on the curation process

This family is new in this Pfam release.

Seed source: PRODOM:PD392219
Previous IDs: none
Type: Family
Author: El-Gebali S
Number in seed: 42
Number in full: 96
Average length of the domain: 76.70 aa
Average identity of full alignment: 94 %
Average coverage of the sequence by the domain: 72.56 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.5 36.4
Noise cut-off 24.1 23.4
Model length: 80
Family (HMM) version: 1
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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 ANAPC16 domain has been found. There are 10 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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