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50  structures 958  species 3  interactions 1632  sequences 11  architectures

Family: AMPKBI (PF04739)

Summary: 5'-AMP-activated protein kinase beta subunit, interaction domain

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 "PRKAB1". More...

PRKAB1 Edit Wikipedia article

PRKAB1
Protein PRKAB1 PDB 1z0m.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases PRKAB1, AMPK, HAMPKb, protein kinase AMP-activated non-catalytic subunit beta 1
External IDs MGI: 1336167 HomoloGene: 38160 GeneCards: PRKAB1
Gene location (Human)
Chromosome 12 (human)
Chr. Chromosome 12 (human)[1]
Chromosome 12 (human)
Genomic location for PRKAB1
Genomic location for PRKAB1
Band 12q24.23 Start 119,667,753 bp[1]
End 119,681,630 bp[1]
RNA expression pattern
PBB GE PRKAB1 201835 s at fs.png

PBB GE PRKAB1 201834 at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_006253

NM_031869

RefSeq (protein)

NP_006244
NP_006244.2

NP_114075

Location (UCSC) Chr 12: 119.67 – 119.68 Mb Chr 5: 116.01 – 116.02 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

5'-AMP-activated protein kinase subunit beta-1 is an enzyme that in humans is encoded by the PRKAB1 gene.[5][6]

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.[6]

Model organisms

Model organisms have been used in the study of PRKAB1 function. A conditional knockout mouse line, called Prkab1tm1a(KOMP)Wtsi[14][15] was generated as part of the International Knockout Mouse Consortium program — a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.[16][17][18]

Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion.[12][19] Twenty five tests were carried out on mutant mice and four significant abnormalities were observed.[12] 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.[12]

Interactions

PRKAB1 has been shown to interact with PRKAG2[20] and PRKAG1.[20]

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.[21] 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.[22]

AMPKBI
Identifiers
Symbol AMPKBI
Pfam PF04739
InterPro IPR006828

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000111725 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000029513 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ 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): 611–4. doi:10.1074/jbc.271.2.611. PMID 8557660. 
  6. ^ a b "Entrez Gene: PRKAB1 protein kinase, AMP-activated, beta 1 non-catalytic subunit". 
  7. ^ "Glucose tolerance test data for Prkab1". Wellcome Trust Sanger Institute. 
  8. ^ "Clinical chemistry data for Prkab1". Wellcome Trust Sanger Institute. 
  9. ^ "Haematology data for Prkab1". Wellcome Trust Sanger Institute. 
  10. ^ "Salmonella infection data for Prkab1". Wellcome Trust Sanger Institute. 
  11. ^ "Citrobacter infection data for Prkab1". Wellcome Trust Sanger Institute. 
  12. ^ a b c d Gerdin AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x. 
  13. ^ Mouse Resources Portal, Wellcome Trust Sanger Institute.
  14. ^ "International Knockout Mouse Consortium". 
  15. ^ "Mouse Genome Informatics". 
  16. ^ 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): 337–342. doi:10.1038/nature10163. PMC 3572410Freely accessible. PMID 21677750. 
  17. ^ Dolgin E (2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi:10.1038/474262a. PMID 21677718. 
  18. ^ Collins FS, Rossant J, Wurst W (2007). "A Mouse for All Reasons". Cell. 128 (1): 9–13. doi:10.1016/j.cell.2006.12.018. PMID 17218247. 
  19. ^ 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 3218837Freely accessible. PMID 21722353. 
  20. ^ a b 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. ENGLAND. 346 (3): 659–69. doi:10.1042/0264-6021:3460659. ISSN 0264-6021. PMC 1220898Freely accessible. PMID 10698692. 
  21. ^ 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): 8675–81. doi:10.1074/jbc.271.15.8675. PMID 8621499. 
  22. ^ 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): 5878–86. PMC 395563Freely accessible. PMID 7813428. 

Further reading

This article incorporates text from the public domain Pfam and InterPro IPR006828

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.

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 [1]. 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 [2]. The isoamylase N-terminal domain (PF02922) is sometimes found in proteins belonging to this family.

Literature references

  1. 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

  2. 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.

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(101)
Full
(1632)
Representative proteomes UniProt
(2296)
NCBI
(2986)
Meta
(2)
RP15
(373)
RP35
(877)
RP55
(1295)
RP75
(1563)
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PP/heatmap 1 View               

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Format an alignment

  Seed
(101)
Full
(1632)
Representative proteomes UniProt
(2296)
NCBI
(2986)
Meta
(2)
RP15
(373)
RP35
(877)
RP55
(1295)
RP75
(1563)
Alignment:
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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
(101)
Full
(1632)
Representative proteomes UniProt
(2296)
NCBI
(2986)
Meta
(2)
RP15
(373)
RP35
(877)
RP55
(1295)
RP75
(1563)
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.

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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: DOMO:DM04946;
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Kerrison ND
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.3 24.3
Trusted cut-off 25.0 24.8
Noise cut-off 23.3 23.3
Model length: 75
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Pkinase CBS CBS

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 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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