Summary: Calcium/calmodulin dependent protein kinase II Association
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Ca2+/calmodulin-dependent protein kinase Edit Wikipedia article
||This article's lead section may not adequately summarize key points of its contents. (July 2012)|
|Calcium/calmodulin dependent protein kinase II association domain|
|crystal structure of calcium/calmodulin-dependent protein kinase|
Ca2+/calmodulin-dependent protein kinases II or CaM kinases II are serine/threonine-specific protein kinases that are regulated by the Ca2+/calmodulin complex. CaMKII is involved in many signaling cascades and is thought to be an important mediator of learning and memory. CaMKII is also necessary for Ca2+ homeostasis and reuptake in cardiomyocytes, chloride transport in epithelia, positive T-cell selection, and CD8 T-cell activation.
There are two types of CaM kinase
- Specialized CaM kinases. An example is the myosin light chain kinase (MLCK) that phosphorylates myosin, causing smooth muscles to contract.
- Multifunctional CaM kinases. Also collectively called CaM kinase II, which play a role in many processes, such as neurotransmitter secretion, transcription factor regulation, and glycogen metabolism.
 Structure, Function, and Autoregulation
Calcium/calmodulin-dependent protein kinase II (CaMKII) is an enzyme that accounts for 1-2% of all of the proteins in the brain. This kinase can exist as 28 different isoforms. The isoforms of CaMKII derive from the alpha, beta, gamma, and delta genes.
 Structural Domains of CaMKII
All of the isoforms of CaMKII have certain core structural components. CaMKII’s structural domains include: a catalytic domain, autoinhibitory domain, variable segment, and self-association domain.
The catalytic domain of CaMKII has several binding sites for ATP and other substrate anchor proteins. It governs the enzyme’s phosphorylation and is shaped in the form of two hexameric rings. The autoinhibitory domain features a pseudosubstrate site. The pseudosubstrate site binds to the protein’s catalytic domain, thus blocking its ability to phosphorylate proteins.
The structural feature that governs this autoinhibition is the Threonine 286 residue. Phosphorylation of this site will permanently activate the CaMKII enzyme. Once the Threonine 286 residue has been phosphorylated, the inhibitory domain is blocked from the pseudosubstrate site. This effectively blocks autoinhibition, allowing for permanent activation of the CaMKII enzyme. This enables CamKII to be active, even in the absence of calcium and calmodulin.
The other two domains in CaMKII are the variable and self-association domains. Differences in these domains contribute to the various CaMKII isoforms.
 Calcium and Calmodulin Dependence of CaMKII
The sensitivity of the CaMKII enzyme to calcium and calmodulin is governed by the variable and self-associative domains. This sensitivity level of CaMKII will also modulate the different states of activation for the enzyme. Initially, the enzyme is activated; however, autophosphorylation does not occur because there is not enough Calcium or calmodulin present to bind to neighboring subunits. As greater amounts of calcium and calmodulin accumulate, autophosphorylation occurs leading to persistent activation of the CaMKII enzyme for a short period of time. However, the Threonine 286 residue eventually becomes dephosphorylated, leading to inactivation of CaMKII.
Autophosphorylation is the process in which a kinase attaches a phosphate group to itself. When CaMKII autophosphorylates, it becomes persistently active. Phosphorylation of the Threonine 286 site allows for the activation of the catalytic domain. Autophosphorylation is enhanced by the structure of the holoenzyme because it is present in two stacked rings. The close proximity of these adjacent rings increases the probability of phosphorylation of neighboring CaMKII enzymes, furthering autophosphorylation. A mechanism that promotes autophosphorylation features inhibition of the PP1 phosphatase. This enables CaMKII to be constantly active by increasing the likelihood of autophosphorylation.
 Long-Term Potentiation
Calcium/ calmodulin dependent protein kinase II is also heavily implicated in long-term potentiation (LTP) – the molecular process of strengthening active synapses that is thought to underlie the processes of memory. It is involved in many aspects of this process. LTP is initiated when the NMDA receptors (which act as “molecular coincidence receptors” and allow this process to be the result of BOTH pre- and post-synaptic neuron activation) allow Ca2+ into the post synaptic neuron. This Ca2+ influx activates CaMKII. It has been shown that there is an increase in CaMKII activity directly in the post synaptic density of dendrites after LTP induction, suggesting that activation is a direct result of stimulation.
 CaMKII is necessary for LTP
When alpha-CaMKII is knocked out in mice, LTP is reduced by 50%. This can be explained by the fact that beta-CaMKII is responsible for approximately 65% of CaMKII activity. LTP can be completely blocked if CaMKII is modified so that it cannot remain active. After LTP induction, CaMKII moves to the postsynaptic density (PSD). However if the stimulation does not induce LTP, the translocation is quickly reversible. Binding to the PSD changes CaMKII so that it is less likely to become dephosphorylated. CaMKII transforms from a substrate for Protein Phosphatase 2A (PP2A), which is responsible for dephosphorylating CaMKII, to that of Protein Phosphatase 1. Strack, S. (1997) demonstrated this phenomenon by chemically stimulating hippocampal slices. This experiment illustrates that CaMKII contributes to the enhancement of synaptic strength. Sanhueza et al. found that persistent activation of CaMKII is necessarily for the maintenance of LTP. He induced LTP in hippocampal slices and experimentally applied an antagonist (CaMKIINtide) to prevent CaMKII from remaining active. The slices that were applied with CaMKIINtide showed a decrease in Normalized EPSP slope after the drug infusion, meaning that the induced LTP reversed itself. The Normalized EPSP slope remained constant in the control; CaMKII continues to be involved in the LTP maintenance process even after LTP establishment. CaMKII is activated by calcium/calmodulin, but it is maintained by autophosphorylation. CaMKII is activated by the NMDA-receptor-mediated Calcium elevation that occurs during LTP induction. Activation is accompanied by phosphorylation of both the alpha and beta-subunits and Thr286/287.
 CaMKII can independently induce LTP
LTP can be induced by artificially injecting CaMKII. When CaMKII is infused in postsynaptically in the hippocampal slices and intracellular perfusion or viral expression, there is a two- to threefold increase in the response of the synapse to glutamate and other chemical signals.
 Mechanistic role in LTP
There is strong evidence that after activation of CaMKII, CaMKII plays a role in the trafficking of AMPA receptors into the membrane and then the PSD of the dendrite. Movement of AMPA receptors increases postsynaptic response to presynaptic depolarization through strengthening the synapses. This produces LTP.
Mechanistically, CaMKII phosphorylates AMPA receptors at the P2 serine 831 site. This increases channel conductance of GluA1 subunits of AMPA receptors, which allows AMPA receptors to be more sensitive than normal during LTP. Increased AMPA receptor sensitivity leads to increase synaptic strength.
In addition to increasing the channel conductance of GluA1 subunits, CaMKII has also been shown to aid in the process of AMPA receptor exocytosis. Reserve AMPA receptors are embedded in endosomes within the cell. CaMKII can stimulate the endosomes to move to the outer membrane and activate the embedded AMPA receptors. Exocytosis of endosomes enlarges and increases the number of AMPA receptors in the synpase. The greater number of AMPA receptors increases the sensitivity of the synapse to presynaptic depolarization, and generates LTP.
 Maintenance of LTP
Along with helping to establish LTP, CaMKII has been shown to be crucial in maintaining LTP. Its ability to autophosphorylate is thought to play an important role in this maintenance. Administration of certain CaMKII blockers has been shown not only to block LTP but also to reverse it in a time dependent manner.
 CaMKII in Behavioral Memory
As LTP is thought to underlie the processes of learning and memory, CaMKII is also crucial to memory formation. Behavioral studies involving genetically engineered mice have demonstrated the importance of CaMKII.
 Preventing Autophosphorylation of CaMKII
 Deficit in Spatial Learning
In 1998, Giese and colleagues studied knockout mice that have been genetically engineered to prevent CaMKII autophosphorylation. They observed that mice had trouble finding the hidden platform in the Morris water maze task. The Morris water maze task is often used to represent hippocampus-dependent spatial learning. The mice’s inability to find the hidden platform implies deficits in spatial learning.
However, these results were not entirely conclusive because memory formation deficit could also be associated with sensory motor impairment resulting from genetic alteration.
 Deficit in Fear Memories
Irvine and colleagues in 2006 showed that preventing autophosphorylation of CaMKII cause mice to have impaired initial learning of fear conditioning. However, after repeated trials, the impaired mice exhibited similar fear memory formation as the control mice. CaMKII may play a role in rapid fear memory, but does not completely prevent fear memory in the long run.
In 2004, Rodrigues and colleagues found that fear conditioning increased phosphorylated CaMKII in lateral amygdala synapses and dendritic spines, indicating that fear conditioning could be responsible for regulating and activating the kinase. They also discovered a drug, KN-62, that inhibited CaMKII and prevented acquisition of fear conditioning and LTP.
 Deficit in Consolidation of Memory Traces
α-CaMKII heterozygous mice express half the normal protein level as the wild-type level. These mice showed normal memory storage in the hippocampus, but deficits in consolidation of memory in the cortex.
 Overexpressing CaMKII
Mayford and colleagues engineered transgenic mice that express CaMKII with a point mutation of Thr-286 to aspartate, which mimics autophosphorylation and increases kinase activity. These mice failed to show LTP response to weak stimuli, and failed to perform hippocampus-dependent spatial learning that depended on visual or olfactory cues.
Researchers speculate these results could be due to lack of stable hippocampal place cells in these animals.
However, because genetic modifications might cause unintentional developmental changes, viral vector delivery allows the mice’s genetic material to be modified at specific stages of development. It is possible with viral vector delivery to inject a specific gene of choice into a particular region of the brain in an already developed animal. Poulsen and colleagues in 2007 used this method to inject CaMKII into the hippocampus. They found that overexpression of CaMKII resulted in slight enhancement of acquisition of new memories.
 Different forms of CaMKII
CaMKIIA is one of the major forms of CamKII. It has been found to play a critical role in sustaining activation of CamKII at the postsynaptic density. Studies have found that knockout mice without CaMKIIA demonstrate a low frequency of LTP. Additionally, these mice do not form persistent, stable place cells in the hippocampus.
CaMK2B has an autophosphorylation site at Thr287. It functions as a targeting or docking module. Reverse transcription-polymerase chain reaction and sequencing analysis identified at least five alternative splicing variants of beta CaMKII (beta, beta6, betae, beta'e, and beta7) in brain and two of them (beta6 and beta7) were first detected in any species.
CaMK2D appears in both neuronal and non-neuronal cell types. It is characterized particularly in many tumor cells, such as a variety of pancreatic, leukemic, breast and other tumor cells. found that CaMK2D is downregulated in human tumor cells.
CaMK2G has been shown to be a crucial extracellular signal-regulated kinase in differentiated smooth muscle cells.
 CaMKII Coding Genes
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- Fährmann, Michael; Kaufhold, Marc-André (2006). "Functional partitioning of epithelial protein kinase CaMKII in signal transduction". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1763: 101–9. doi:10.1016/j.bbamcr.2005.11.012.
- McGargill, Maureen A.; Sharp, Leslie L.; Bui, Jack D.; Hedrick, Stephen M.; Calbo, Sébastien (July 2005). "Active Ca2+/calmodulin-dependent protein kinase II gamma B impairs positive selection of T cells by modulating TCR signaling". The Journal of Immunology 175 (2): 656–64. PMID 16002660.
- Lin, Meei Yun; Zal, Tomasz; Ch’en, Irene L.; Gascoigne, Nicholas R. J.; Hedrick, Stephen M. (May 2005). "A pivotal role for the multifunctional calcium/calmodulin-dependent protein kinase II in T cells: from activation to unresponsiveness". The Journal of Immunology 174 (9): 5583–92. PMID 15843557.
- Yamauchi, Takashi (August 2005). "Neuronal Ca2+/calmodulin-dependent protein kinase II—discovery, progress in a quarter of a century, and perspective: implication for learning and memory". Biological & Pharmaceutical Bulletin 28 (8): 1342–54. doi:10.1248/bpb.28.1342. PMID 16079472.
- Hudmon, Andy; Schulman, Howard (2002). "NEURONALCA2+/CALMODULIN-DEPENDENTPROTEINKINASEII: The Role of Structure and Autoregulation in Cellular Function". Annual Review of Biochemistry 71: 473–510. doi:10.1146/annurev.biochem.71.110601.135410. PMID 12045104.
- Kanaseki, T; Ikeuchi, Y; Sugiura, H; Yamauchi, T (1991). "Structural features of Ca2+/calmodulin-dependent protein kinase II revealed by electron microscopy". The Journal of Cell Biology 115 (4): 1049–60. doi:10.1083/jcb.115.4.1049. PMC 2289961. PMID 1659571.
- Yang, E; Schulman, H (1999). "Structural examination of autoregulation of multifunctional calcium/calmodulin-dependent protein kinase II". The Journal of Biological Chemistry 274 (37): 26199–208. doi:10.1074/jbc.274.37.26199. PMID 10473573.
- Giese, K. P. (1998). "Autophosphorylation at Thr286 of the Calcium-Calmodulin Kinase II in LTP and Learning". Science 279 (5352): 26199–208. doi:10.1126/science.279.5352.870. PMID 9452388.
- Griffith LC, Lu CS, Sun XX (October 2003). "CaMKII, an enzyme on the move: regulation of temporospatial localization". Mol. Interv. 3 (7): 386–403. doi:10.1124/mi.3.7.386. PMID 14993460.
- Lisman, J (1994). "The CaM kinase II hypothesis for the storage of synaptic memory". Trends in neurosciences 17 (10): 406–12. doi:10.1016/0166-2236(94)90014-0. PMID 7530878.
- Blitzer, Robert D.; Wong, Tony; Nouranifar, Rabin; Iyengar, Ravi; Landau, Emmanuel M. (1995). "Postsynaptic CAMP pathway gates early LTP in hippocampal CA1 region". Neuron 15 (6): 1403–14. doi:10.1016/0896-6273(95)90018-7. PMID 8845163.
- Giese, K. P.; Fedorov, NB; Filipkowski, RK; Silva, AJ (1998). "Autophosphorylation at Thr286 of the Calcium-Calmodulin Kinase II in LTP and Learning". Science 279 (5352): 870–3. doi:10.1126/science.279.5352.870. PMID 9452388.
- Strack, S.; Choi, S; Lovinger, DM; Colbran, RJ (1997). "Translocation of Autophosphorylated Calcium/Calmodulin-dependent Protein Kinase II to the Postsynaptic Density". Journal of Biological Chemistry 272 (21): 13467–70. doi:10.1074/jbc.272.21.13467. PMID 9153188.
- Gardoni, F; Schrama, LH; Kamal, A; Gispen, WH; Cattabeni, F; Di Luca, M (2001). "Hippocampal synaptic plasticity involves competition between Ca2+/calmodulin-dependent protein kinase II and postsynaptic density 95 for binding to the NR2A subunit of the NMDA receptor". The Journal of neuroscience : the official journal of the Society for Neuroscience 21 (5): 1501–9. PMID 11222640.
- Silva, A.; Stevens, C.; Tonegawa, S; Wang, Y (1992). "Deficient hippocampal long-term potentiation in alpha-calcium-calmodulin kinase II mutant mice". Science 257 (5067): 201–6. doi:10.1126/science.1378648. PMID 1378648.
- . pp. 344–54. doi:10.1101/lm.5.4.344. Citation has no title
- Hrabetova, S; Sacktor, TC (1996). "Bidirectional regulation of protein kinase M zeta in the maintenance of long-term potentiation and long-term depression". The Journal of neuroscience : the official journal of the Society for Neuroscience 16 (17): 5324–33. PMID 8757245.
- Sanhueza, M; McIntyre, CC; Lisman, JE (2007). "Reversal of synaptic memory by Ca2+/calmodulin-dependent protein kinase II inhibitor". The Journal of neuroscience : the official journal of the Society for Neuroscience 27 (19): 5190–9. doi:10.1523/JNEUROSCI.5049-06.2007. PMID 17494705.
- Davies, SN; Lester, RA; Reymann, KG; Collingridge, GL (1989). "Temporally distinct pre- and post-synaptic mechanisms maintain long-term potentiation". Nature 338 (6215): 500–3. doi:10.1038/338500a0. PMID 2564640.
- Montgomery, JM; Pavlidis, P; Madison, DV (2001). "Pair recordings reveal all-silent synaptic connections and the postsynaptic expression of long-term potentiation". Neuron 29 (3): 691–701. doi:10.1016/S0896-6273(01)00244-6. PMID 11301028.
- Collingridge, Graham L.; Benke, Tim A.; Lüthi, Andreas; Isaac, John T. R. (1998). "Modulation of AMPA receptor unitary conductance by synaptic activity". Nature 393 (6687): 793–7. doi:10.1038/31709. PMID 9655394.
- Lisman, John; Schulman, Howard; Cline, Hollis (2002). "THE MOLECULAR BASIS OF CaMKII FUNCTION IN SYNAPTIC AND BEHAVIOURAL MEMORY". Nature Reviews Neuroscience 3 (3): 175–90. doi:10.1038/nrn753. PMID 11994750.
- Yang, H.-W.; Hu, XD; Zhang, HM; Xin, WJ; Li, MT; Zhang, T; Zhou, LJ; Liu, XG (2003). "Roles of CaMKII, PKA, and PKC in the Induction and Maintenance of LTP of C-Fiber-Evoked Field Potentials in Rat Spinal Dorsal Horn". Journal of Neurophysiology 91 (3): 1122–33. doi:10.1152/jn.00735.2003. PMID 14586032.
- Rudy, Jerry W. (2004). The Neurobiology of Learning and Memory. Snauer. ISBN 978-0-87893-669-4. [page needed]
- Irvine, Elaine E.; Von Hertzen, Laura S.J.; Plattner, Florian; Giese, Karl Peter (2006). "αCaMKII autophosphorylation: a fast track to memory". Trends in Neurosciences 29 (8): 459–65. doi:10.1016/j.tins.2006.06.009. PMID 16806507.
- Rodrigues, S. M.; Farb, CR; Bauer, EP; Ledoux, JE; Schafe, GE (2004). "Pavlovian Fear Conditioning Regulates Thr286 Autophosphorylation of Ca2+/Calmodulin-Dependent Protein Kinase II at Lateral Amygdala Synapses". Journal of Neuroscience 24 (13): 3281–8. doi:10.1523/JNEUROSCI.5303-03.2004. PMID 15056707.
- Frankland, Paul W.; O'Brien, Cara; Ohno, Masuo; Kirkwood, Alfredo; Silva, Alcino J. (2001). "Alpha-CaMKII-dependent plasticity in the cortex is required for permanent memory". Nature 411 (6835): 309–13. doi:10.1038/35077089. PMID 11357133.
- Mayford, Mark; Wang, Jian; Kandel, Eric R; O'Dell, Thomas J (1995). "CaMKII regulates the frequency-response function of hippocampal synapses for the production of both LTD and LTP". Cell 81 (6): 891–904. doi:10.1016/0092-8674(95)90009-8. PMID 7781066.
- Rotenberg, Alexander; Mayford, Mark; Hawkins, Robert D; Kandel, Eric R; Muller, Robert U (1996). "Mice Expressing Activated CaMKII Lack Low Frequency LTP and Do Not Form Stable Place Cells in the CA1 Region of the Hippocampus". Cell 87 (7): 1351–61. doi:10.1016/S0092-8674(00)81829-2. PMID 8980240.
- Poulsen, D.J.; Standing, D.; Bullshields, K.; Spencer, K.; Micevych, P.E.; Babcock, A.M. (2007). "Overexpression of hippocampal Ca2+/calmodulin-dependent protein kinase II improves spatial memory". Journal of Neuroscience Research 85 (4): 735–9. doi:10.1002/jnr.21163. PMID 17171706.
- Soderling, T (2000). "CaM-kinases: modulators of synaptic plasticity". Current Opinion in Neurobiology 10 (3): 375–80. doi:10.1016/S0959-4388(00)00090-8. PMID 10851169.
- Wang, P; Wu, YL; Zhou, TH; Sun, Y; Pei, G (2000). "Identification of alternative splicing variants of the β subunit of human Ca2+/calmodulin-dependent protein kinase II with different activities". FEBS Letters 475 (2): 107–10. doi:10.1016/S0014-5793(00)01634-3. PMID 10858498.
- Wang, P; Wu, YL; Zhou, TH; Sun, Y; Pei, G (2000). "Identification of alternative splicing variants of the β subunit of human Ca2+/calmodulin-dependent protein kinase II with different activities". FEBS Letters 475 (2): 1–11. doi:10.1016/S0014-5793(00)01634-3. PMID 10858498.
- Marganski, W. A.; Gangopadhyay, SS; Je, HD; Gallant, C; Morgan, KG (2005). "Targeting of a Novel Ca+2/Calmodulin-Dependent Protein Kinase II Is Essential for Extracellular Signal-Regulated Kinase-Mediated Signaling in Differentiated Smooth Muscle Cells". Circulation Research 97 (6): 541–549. doi:10.1161/01.RES.0000182630.29093.0d. PMID 16109919.
- Calcium-Calmodulin Dependent Protein Kinases at the US National Library of Medicine Medical Subject Headings (MeSH)
- To learn more about the CaMKII ...
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Calcium/calmodulin dependent protein kinase II Association Provide feedback
This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (PF00069) at their N-terminus . The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers .
Gangopadhyay SS, Barber AL, Gallant C, Grabarek Z, Smith JL, Morgan KG; , Biochem J 2003;372:347-357.: Differential functional properties of calmodulin-dependent protein kinase IIgamma variants isolated from smooth muscle. PUBMED:12603201 EPMC:12603201
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013543
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity [PUBMED:3291115]:
- Serine/threonine-protein kinases
- Tyrosine-protein kinases
- Dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins)
Protein kinase function is evolutionarily conserved from Escherichia coli to human [PUBMED:12471243]. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation [PUBMED:12368087]. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [PUBMED:15078142], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases [PUBMED:15320712].
This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (INTERPRO) at their N terminus [PUBMED:12603201]. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [PUBMED:14993460] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||calmodulin-dependent protein kinase activity (GO:0004683)|
|calmodulin binding (GO:0005516)|
|Biological process||protein phosphorylation (GO:0006468)|
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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.
|Seed source:||Pfam-B_1025 (release 18.0)|
|Number in seed:||7|
|Number in full:||782|
|Average length of the domain:||118.40 aa|
|Average identity of full alignment:||52 %|
|Average coverage of the sequence by the domain:||32.17 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
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 is 1 interaction 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 CaMKII_AD domain has been found. There are 44 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...