FB2021_03, released June 15, 2021

Gene: Dmel\Pdk

Open Close
General Information
Symbol
Dmel\Pdk
Species
D. melanogaster
Name
Pyruvate dehydrogenase kinase
Annotation Symbol
CG8808
Feature Type
protein_coding_gene
FlyBase ID
FBgn0017558
Gene Model Status
Current
Stock Availability
9 publicly available
Enzyme Name (EC)
[Pyruvate dehydrogenase (acetyl-transferring)] kinase (2.7.11.2)
Gene Summary
Inhibits the mitochondrial pyruvate dehydrogenase complex by phosphorylation of the E1 alpha subunit, thus contributing to the regulation of glucose metabolism. (UniProt, P91622)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

DmPdk

Key Links
Genomic Location
Cytogenetic map
45D5-45D7
Sequence location
2R:9,426,439..9,434,638 [+]
Recombination map
2-60
RefSeq locus
NT_033778 REGION:9426439..9434638
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (6 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables protein kinase activity
inferred from sequence or structural similarity with UniProtKB:Q15118
(FlyBase Curators, 2008--)
enables pyruvate dehydrogenase (acetyl-transferring) kinase activity
inferred from biological aspect of ancestor with PANTHER:PTN000236514
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with UniProtKB:Q9JK42
(FlyBase Curators, 2008--)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in protein phosphorylation
inferred from biological aspect of ancestor with PANTHER:PTN000236514
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in regulation of glucose metabolic process
inferred from sequence or structural similarity with UniProtKB:Q9JK42
(FlyBase Curators, 2008--)
inferred from biological aspect of ancestor with PANTHER:PTN000236514
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of mitochondrial pyruvate dehydrogenase complex
inferred from sequence or structural similarity with UniProtKB:Q9JK42
(FlyBase Curators, 2008--)
is_active_in mitochondrion
inferred from biological aspect of ancestor with PANTHER:PTN000236514
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the PDK/BCKDK protein kinase family. (P91622)
Protein Signatures (InterPro)
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
ATP + [pyruvate dehydrogenase (acetyl-transferring)] = ADP + [pyruvate dehydrogenase (acetyl-transferring)] phosphate (2.7.11.2)
Summaries
Gene Group (FlyBase)
ATYPICAL PROTEIN KINASES -
Atypical kinases are protein kinases or putative protein kinases that do not share clear sequence similarity with conventional eukaryotic protein kinases, but they or their orthologs have been shown experimentally to have protein kinase activity. Atypical kinases are defined in FBrf0201870.
Protein Function (UniProtKB)
Inhibits the mitochondrial pyruvate dehydrogenase complex by phosphorylation of the E1 alpha subunit, thus contributing to the regulation of glucose metabolism.
(UniProt, P91622)
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\Pdk for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Pdk-RA
FBtr0088508
NM_057867
2080
413
Pdk-RB
FBtr0112892
NM_001103770
2293
422
Pdk-RC
FBtr0306807
NM_001259295
2732
413
Pdk-RD
FBtr0333004
NM_001273896
2440
415
Additional Transcript Data and Comments
Reported size (kB)

2.7, 2.1 (northern blot)

(Katsube et al., 1997)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
Pdk-PA
FBpp0087592
46.6
413
7.16
NP_477215
AAF58938
Pdk-PB
FBpp0111805
47.6
422
6.45
NP_001097240
ABV53737
Pdk-PC
FBpp0297719
46.6
413
7.16
NP_001246224
AFH07979
Pdk-PD
FBpp0305219
47.1
415
6.84
NP_001260825
AGB93358
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

413 aa isoforms: Pdk-PA, Pdk-PC
Additional Polypeptide Data and Comments
Reported size (kDa)

413 (aa)

(Katsube et al., 1997)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Pdk using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
organism | ubiquitous
(Katsube et al., 1997)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 17

Comment: reference states 0-20 hr AEL

(Katsube et al., 1997)
third instar larval stage
(Katsube et al., 1997)
pupal stage
(Katsube et al., 1997)
adult stage | female
(Katsube et al., 1997)
adult stage | male
(Katsube et al., 1997)
Additional Descriptive Data

Pdk transcript is distributed ubiquitously in embryos.

(Katsube et al., 1997)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Pdk in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB
EMBL-EBI Single Cell Expression Atlas
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 11 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pdk
Transgenic constructs containing regulatory region of Pdk
Aberrations (Deficiencies and Duplications) ( 6 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
female semi-sterile, with Scer\GAL4VP16.mat.αTub67C
fertile
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (5)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\PDK3
14 of 15
Yes
Yes
1  
Hsap\PDK1
13 of 15
No
Yes
Hsap\PDK2
13 of 15
No
Yes
1  
Hsap\PDK4
12 of 15
No
Yes
1  
Hsap\BCKDK
2 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (5)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Pdk3
14 of 15
Yes
Yes
Mmus\Pdk2
13 of 15
No
Yes
Mmus\Pdk1
12 of 15
No
Yes
Mmus\Pdk4
12 of 15
No
Yes
Mmus\Bckdk
2 of 15
No
Yes
Rattus norvegicus (Norway rat) (5)
Rnor\Pdk1
12 of 13
Yes
Yes
Rnor\Pdk3
12 of 13
Yes
Yes
Rnor\Pdk2
11 of 13
No
Yes
Rnor\Pdk4
11 of 13
No
Yes
Rnor\Bckdk
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
Xtro\pdk4
9 of 12
Yes
Yes
Xtro\pdk1
8 of 12
No
Yes
Xtro\pdk3
8 of 12
No
Yes
Xtro\bckdk
2 of 12
No
Yes
Danio rerio (Zebrafish) (7)
Drer\pdk1
13 of 15
Yes
Yes
Drer\pdk2a
13 of 15
Yes
Yes
Drer\pdk2b
9 of 15
No
Yes
Drer\pdk3a
9 of 15
No
Yes
Drer\pdk4
9 of 15
No
Yes
Drer\pdk3b
5 of 15
No
Yes
Drer\bckdk
2 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\pdhk-2
14 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\PDK
8 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (5)
Scer\PKP1
7 of 15
Yes
Yes
Scer\PKP2
5 of 15
No
Yes
Scer\SKN7
1 of 15
No
No
Scer\SLN1
1 of 15
No
Yes
Scer\SSK1
1 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\pkp1
11 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919084Z )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00003356
Drosophila simulans
Dsim\GD10655
Drosophila sechellia
Dsec\GM21122
Drosophila erecta
Dere\GG24073
Drosophila yakuba
Dyak\GE19277
Drosophila ananassae
Dana\GF12464
Drosophila pseudoobscura pseudoobscura
Dpse\GA30459
Drosophila persimilis
Dper\GL17352
Drosophila willistoni
Dwil\GK15747
Drosophila virilis
Dvir\GJ15047
Drosophila mojavensis
Dmoj\GI19876
Drosophila grimshawi
Dgri\GH19919
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915051K )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17009319
Glossina morsitans
Tsetse fly
Gmor\GMOY012319
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_02433
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL007375
Anopheles darlingi
American malaria mosquito
Adar\ADAC005466
Anopheles gambiae
Malaria mosquito
Agam\AGAP010276
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ013528
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04PC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA003258
Danaus plexippus
Monarch butterfly
Dple\DPOGS210186-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL009526
Apis florea
Little honeybee
Aflo\2227414068
Apis mellifera
Western honey bee
Amel\Pdk
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP23458
Bombus terrestris
Buff-tailed bumblebee
Bter\15210191
Linepithema humile
Argentine ant
Lhum\LH12918
Linepithema humile
Argentine ant
Lhum\LH12925
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0017ab
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG003343
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_11307
Tribolium castaneum
Red flour beetle
Tcas\TC009468
Pediculus humanus
Human body louse
Phum\PHUM574180
Rhodnius prolixus
Kissing bug
Rpro\RPRC013269
Cimex lectularius
Bed bug
Clec\CLEC001870
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI007190
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_01337
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X07QN )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR012808
Ixodes scapularis
Black-legged tick
Isca\ISCW013649
Stegodyphus mimosarum
African social velvet spider
Smim\KFM76176.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur11g03710
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_240818
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G07DJ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Pdk2
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000001943
Gallus gallus
Domestic chicken
Ggal\PDK4
Gallus gallus
Domestic chicken
Ggal\LOC425178
Gallus gallus
Domestic chicken
Ggal\PDK3
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 1 )
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    PdkGL00009
    ameliorates  neurodegeneration with brain iron accumulation
    modeled by PpcdcKK109377
    (Lambrechts et al., 2019)
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    PDK3; pyruvate dehydrogenase kinase 3
    14 of 15
    300906
     
    PDK1; pyruvate dehydrogenase kinase 1
    13 of 15
    602524
        PDK2; pyruvate dehydrogenase kinase 2
        13 of 15
        602525
             
            PDK4; pyruvate dehydrogenase kinase 4
            12 of 15
            602527
                 
                Functional Complementation Data
                Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
                Interactions
                Summary of Physical Interactions
                esyN Network Diagram
                Interactions Browser
                Summary of Genetic Interactions
                esyN Network Diagram
                esyN Network Key:
                Suppression
                Enhancement
                View in Interactions Browser
                Please look at the allele data for full details of the genetic interactions
                Starting gene(s)
                Interaction type
                Interacting gene(s)
                Reference
                Starting gene(s)
                Interaction type
                Interacting gene(s)
                Reference
                Syx1A
                suppressible
                Pdk
                (van Swinderen and Greenspan, 2005)
                External Data
                Linkouts
                BioGRID - A database of protein and genetic interactions.
                DroID - A comprehensive database of gene and protein interactions.
                InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
                Pathways
                Signaling Pathways (FlyBase)
                Metabolic Pathways
                External Data
                Linkouts
                Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                Genomic Location and Detailed Mapping Data
                Chromosome (arm)
                2R
                Recombination map
                2-60
                Cytogenetic map
                45D5-45D7
                Sequence location
                2R:9,426,439..9,434,638 [+]
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                45D5-45D7
                Limits computationally determined from genome sequence between P{lacW}wunk09507&P{lacW}l(2)k12402k12402 and P{EP}EP2165&P{lacW}l(2)k01301k01301
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                45C1-45D10
                (Katsube, 1996.11.5)
                45C-45D
                (determined by in situ hybridisation)
                (Katsube et al., 1997)
                Experimentally Determined Recombination Data
                Location

                2-60

                (FlyBase, 2016)

                2-59.1

                (Comeron et al., 2012)

                2-

                (Katsube, 1996.11.5)
                Left of (cM)
                Right of (cM)
                Notes
                Stocks and Reagents
                Stocks (9)
                Genomic Clones (14)
                 

                Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

                cDNA Clones (155)
                 

                Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

                cDNA clones, fully sequenced
                BDGP DGC clones
                Other clones
                Drosophila Genomics Resource Center cDNA clones

                For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

                cDNA Clones, End Sequenced (ESTs)
                BDGP DGC clones
                Other clones
                RNAi and Array Information
                Linkouts
                DRSC - Results frm RNAi screens
                GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                Antibody Information
                Laboratory Generated Antibodies
                 
                Commercially Available Antibodies
                 
                Other Information
                Relationship to Other Genes
                Source for database identify of
                Source for database merge of

                Source for merge of: Pdk BcDNA:LD09837

                (FlyBase, 1996-)
                Additional comments

                Source for merge of Pdk BcDNA:LD09837 was a shared cDNA ( date:030728 ).

                (FlyBase, 1996-)
                Other Comments

                dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

                (Kiger et al., 2003)

                Cloning and characterisation of Pdk.

                (Katsube et al., 1997)
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 59 )
                Sequence Crossreferences
                NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
                GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
                GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
                RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
                UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
                UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
                Other crossreferences
                Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                DRscDB
                EMBL-EBI Single Cell Expression Atlas
                Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                Flygut - An atlas of the Drosophila adult midgut
                GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                InterPro - A database of protein families, domains and functional sites
                KEGG Genes - Molecular building blocks of life in the genomic space.
                MARRVEL_MODEL
                modMine - A data warehouse for the modENCODE project
                Linkouts
                BioGRID - A database of protein and genetic interactions.
                DroID - A comprehensive database of gene and protein interactions.
                DRSC - Results frm RNAi screens
                FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                FlyMine - An integrated database for Drosophila genomics
                InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
                Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                Synonyms and Secondary IDs (10)
                Datasets (0)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                References (92)