Summary: 5'-AMP-activated protein kinase beta subunit, interaction domain
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PRKAB1 Edit Wikipedia article
|, AMPK, HAMPKb, protein kinase AMP-activated non-catalytic subunit beta 1|
The protein encoded by this gene is a regulatory subunit of the AMP-activated protein kinase (AMPK). AMPK is a heterotrimer consisting of an alpha catalytic subunit, and non-catalytic beta and gamma subunits. AMPK is an important energy-sensing enzyme that monitors cellular energy status. In response to cellular metabolic stresses, AMPK is activated, and thus phosphorylates and inactivates acetyl-CoA carboxylase (ACC) and beta-hydroxy beta-methylglutaryl-CoA reductase (HMGCR), key enzymes involved in regulating de novo biosynthesis of fatty acid and cholesterol. This subunit may be a positive regulator of AMPK activity. The myristoylation and phosphorylation of this subunit have been shown to affect the enzyme activity and cellular localization of AMPK. This subunit may also serve as an adaptor molecule mediating the association of the AMPK complex.
|Recessive lethal study||Normal|
|Glucose tolerance test||Abnormal|
|Auditory brainstem response||Normal|
|Peripheral blood lymphocytes||Normal|
|All tests and analysis from|
Model organisms have been used in the study of PRKAB1 function. A conditional knockout mouse line, called Prkab1tm1a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program â€” a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty five tests were carried out on mutant mice and four significant abnormalities were observed. Homozygous mutant males displayed impaired glucose tolerance. Animals of both sex had increased circulating bilirubin levels, increased IgG3 levels, and a number of atypical haematology parameters.
The 5'-AMP-activated protein kinase beta subunit interaction domain (AMPKBI) is a conserved domain found in the beta subunit of the 5-AMP-activated protein kinase complex, and its yeast homologues Sip1 (SNF1-interacting protein 1), Sip2 (SNF1-interacting protein 2) and Gal83 (galactose metabolism 83), which are found in the SNF1 (sucrose non-fermenting) kinase complex. This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known.
- GRCh38: Ensembl release 89: ENSG00000111725 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000029513 - Ensembl, May 2017
- "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- Stapleton D, Mitchelhill KI, Gao G, Widmer J, Michell BJ, Teh T, House CM, Fernandez CS, Cox T, Witters LA, Kemp BE (February 1996). "Mammalian AMP-activated protein kinase subfamily". J Biol Chem. 271 (2): 611â€“4. doi:10.1074/jbc.271.2.611. PMID 8557660.
- "Entrez Gene: PRKAB1 protein kinase, AMP-activated, beta 1 non-catalytic subunit".
- "Glucose tolerance test data for Prkab1". Wellcome Trust Sanger Institute.
- "Clinical chemistry data for Prkab1". Wellcome Trust Sanger Institute.
- "Haematology data for Prkab1". Wellcome Trust Sanger Institute.
- "Salmonella infection data for Prkab1". Wellcome Trust Sanger Institute.
- "Citrobacter infection data for Prkab1". Wellcome Trust Sanger Institute.
- Gerdin AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925â€“7. doi:10.1111/j.1755-3768.2010.4142.x.
- Mouse Resources Portal, Wellcome Trust Sanger Institute.
- "International Knockout Mouse Consortium".
- "Mouse Genome Informatics".
- Skarnes, W. C.; Rosen, B.; West, A. P.; Koutsourakis, M.; Bushell, W.; Iyer, V.; Mujica, A. O.; Thomas, M.; Harrow, J.; Cox, T.; Jackson, D.; Severin, J.; Biggs, P.; Fu, J.; Nefedov, M.; De Jong, P. J.; Stewart, A. F.; Bradley, A. (2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337â€“342. doi:10.1038/nature10163. PMC 3572410. PMID 21677750.
- Dolgin E (2011). "Mouse library set to be knockout". Nature. 474 (7351): 262â€“3. doi:10.1038/474262a. PMID 21677718.
- Collins FS, Rossant J, Wurst W (2007). "A Mouse for All Reasons". Cell. 128 (1): 9â€“13. doi:10.1016/j.cell.2006.12.018. PMID 17218247.
- van der Weyden L, White JK, Adams DJ, Logan DW (2011). "The mouse genetics toolkit: revealing function and mechanism". Genome Biol. 12 (6): 224. doi:10.1186/gb-2011-12-6-224. PMC 3218837. PMID 21722353.
- Cheung, P C; Salt I P; Davies S P; Hardie D G; Carling D (March 2000). "Characterization of AMP-activated protein kinase gamma-subunit isoforms and their role in AMP binding". Biochem. J. 346 (3): 659â€“69. doi:10.1042/0264-6021:3460659. ISSN 0264-6021. PMC 1220898. PMID 10698692.
- Gao G, Fernandez CS, Stapleton D, Auster AS, Widmer J, Dyck JR, Kemp BE, Witters LA (April 1996). "Non-catalytic beta- and gamma-subunit isoforms of the 5'-AMP-activated protein kinase". J. Biol. Chem. 271 (15): 8675â€“81. doi:10.1074/jbc.271.15.8675. PMID 8621499.
- Yang X, Jiang R, Carlson M (December 1994). "A family of proteins containing a conserved domain that mediates interaction with the yeast SNF1 protein kinase complex". EMBO J. 13 (24): 5878â€“86. doi:10.1002/j.1460-2075.1994.tb06933.x. PMC 395563. PMID 7813428.
- Carling D (2004). "The AMP-activated protein kinase cascade--a unifying system for energy control". Trends Biochem. Sci. 29 (1): 18â€“24. doi:10.1016/j.tibs.2003.11.005. PMID 14729328.
- Gao G, Fernandez CS, Stapleton D, et al. (1996). "Non-catalytic beta- and gamma-subunit isoforms of the 5'-AMP-activated protein kinase". J. Biol. Chem. 271 (15): 8675â€“81. doi:10.1074/jbc.271.15.8675. PMID 8621499.
- Woods A, Cheung PC, Smith FC, et al. (1996). "Characterization of AMP-activated protein kinase beta and gamma subunits. Assembly of the heterotrimeric complex in vitro". J. Biol. Chem. 271 (17): 10282â€“90. doi:10.1074/jbc.271.48.30517. PMID 8626596.
- Dyck JR, Gao G, Widmer J, et al. (1996). "Regulation of 5'-AMP-activated protein kinase activity by the noncatalytic beta and gamma subunits". J. Biol. Chem. 271 (30): 17798â€“803. doi:10.1074/jbc.271.30.17798. PMID 8663446.
- Stapleton D, Woollatt E, Mitchelhill KI, et al. (1997). "AMP-activated protein kinase isoenzyme family: subunit structure and chromosomal location". FEBS Lett. 409 (3): 452â€“6. doi:10.1016/S0014-5793(97)00569-3. PMID 9224708.
- Mitchelhill KI, Michell BJ, House CM, et al. (1997). "Posttranslational modifications of the 5'-AMP-activated protein kinase beta1 subunit". J. Biol. Chem. 272 (39): 24475â€“9. doi:10.1074/jbc.272.39.24475. PMID 9305909.
- Thornton C, Snowden MA, Carling D (1998). "Identification of a novel AMP-activated protein kinase beta subunit isoform that is highly expressed in skeletal muscle". J. Biol. Chem. 273 (20): 12443â€“50. doi:10.1074/jbc.273.20.12443. PMID 9575201.
- Cheung PC, Salt IP, Davies SP, et al. (2000). "Characterization of AMP-activated protein kinase gamma-subunit isoforms and their role in AMP binding". Biochem. J. 346 (3): 659â€“69. doi:10.1042/0264-6021:3460659. PMC 1220898. PMID 10698692.
- da Silva Xavier G, Leclerc I, Salt IP, et al. (2000). "Role of AMP-activated protein kinase in the regulation by glucose of islet beta cell gene expression". Proc. Natl. Acad. Sci. U.S.A. 97 (8): 4023â€“8. Bibcode:2000PNAS...97.4023D. doi:10.1073/pnas.97.8.4023. PMC 18135. PMID 10760274.
- Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899â€“903. Bibcode:2002PNAS...9916899M. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
- Lemieux K, Konrad D, Klip A, Marette A (2003). "The AMP-activated protein kinase activator AICAR does not induce GLUT4 translocation to transverse tubules but stimulates glucose uptake and p38 mitogen-activated protein kinases alpha and beta in skeletal muscle". FASEB J. 17 (12): 1658â€“65. doi:10.1096/fj.02-1125com. PMID 12958172.
- Landree LE, Hanlon AL, Strong DW, et al. (2004). "C75, a fatty acid synthase inhibitor, modulates AMP-activated protein kinase to alter neuronal energy metabolism". J. Biol. Chem. 279 (5): 3817â€“27. doi:10.1074/jbc.M310991200. PMID 14615481.
- Inoki K, Zhu T, Guan KL (2004). "TSC2 mediates cellular energy response to control cell growth and survival". Cell. 115 (5): 577â€“90. doi:10.1016/S0092-8674(03)00929-2. PMID 14651849.
- Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40â€“5. doi:10.1038/ng1285. PMID 14702039.
- Andersson U, Filipsson K, Abbott CR, et al. (2004). "AMP-activated protein kinase plays a role in the control of food intake" (PDF). J. Biol. Chem. 279 (13): 12005â€“8. doi:10.1074/jbc.C300557200. PMID 14742438.
- Pilon G, Dallaire P, Marette A (2004). "Inhibition of inducible nitric-oxide synthase by activators of AMP-activated protein kinase: a new mechanism of action of insulin-sensitizing drugs". J. Biol. Chem. 279 (20): 20767â€“74. doi:10.1074/jbc.M401390200. PMID 14985344.
- Shaw RJ, Kosmatka M, Bardeesy N, et al. (2004). "The tumor suppressor LKB1 kinase directly activates AMP-activated kinase and regulates apoptosis in response to energy stress". Proc. Natl. Acad. Sci. U.S.A. 101 (10): 3329â€“35. Bibcode:2004PNAS..101.3329S. doi:10.1073/pnas.0308061100. PMC 373461. PMID 14985505.
- Kim EK, Miller I, Aja S, et al. (2004). "C75, a fatty acid synthase inhibitor, reduces food intake via hypothalamic AMP-activated protein kinase". J. Biol. Chem. 279 (19): 19970â€“6. doi:10.1074/jbc.M402165200. PMID 15028725.
- PDBe-KB provides an overview of all the structure information available in the PDB for Human 5'-AMP-activated protein kinase subunit beta-1 (PRKAB1)
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.
5'-AMP-activated protein kinase beta subunit, interaction domain Provide feedback
This region is found in the beta subunit of the 5'-AMP-activated protein kinase complex, and its yeast homologues Sip1, Sip2 and Gal83, which are found in the SNF1 kinase complex . This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known . The isoamylase N-terminal domain (PF02922) is sometimes found in proteins belonging to this family.
Gao G, Fernandez CS, Stapleton D, Auster AS, Widmer J, Dyck JR, Kemp BE, Witters LA; , J Biol Chem 1996;271:8675-8681.: Non-catalytic beta- and gamma-subunit isoforms of the 5'-AMP-activated protein kinase. PUBMED:8621499 EPMC:8621499
Yang X, Jiang R, Carlson M; , EMBO J 1994;13:5878-5886.: A family of proteins containing a conserved domain that mediates interaction with the yeast SNF1 protein kinase complex. PUBMED:7813428 EPMC:7813428
This tab holds annotation information from the InterPro database.
InterPro entry IPR006828
Association with the SNF1 complex (ASC) domain is found in the Sip1/Sip2/Gal83/AMPKbeta subunits of the SNF1/AMP-activated protein kinase (AMPK) complex [PUBMED:11252725]. SNF1/AMPK are heterotrimeric enzymes composed of a catalytic alpha-subunit, a regulatory gamma-subunit and a regulatory/targeting beta-subunit [PUBMED:9121458]. Saccharomyces cerevisiae encodes three beta-subunit genes, Sip1, Sip2 and Gal83 [PUBMED:7813428, PUBMED:10990457]. The beta-subunits function as target selective adaptors that recruit the catalytic kinase and regulator Snf4/gamma-subunits. The ASC domain is required for interaction with Snf4 [PUBMED:11252725, PUBMED:9121458].
The SNF1 kinase complex is required for transcriptional, metabolic, and developmental adaptations in response to glucose limitation [PUBMED:17981722, PUBMED:10207618]. As glucose levels decrease, Snf1 is activated and promotes the use of alternative carbon sources.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||protein binding (GO:0005515)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
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You can see the alignments as HTML or in three different sequence viewers:
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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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.
|Number in seed:||101|
|Number in full:||1632|
|Average length of the domain:||75.60 aa|
|Average identity of full alignment:||46 %|
|Average coverage of the sequence by the domain:||21.73 %|
|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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- 0 sequences
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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:
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There are 3 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 AMPKBI domain has been found. There are 50 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.
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