RefGenome Electronic Jamboree 2008-10 PFKL

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Contents

Orthoset

Ortholog set at PPOD

Participants

NameGroupOrganism(s)/Genome(s)Notes

Susan Tweedie

flyBase

D. melanogaster

FBgn0003071

Kimberly Van Auken

WormBase

C. elegans

Working on PFKL ortholog C50F4.2 = WBGene00008230

Rachael Huntley

GOA

Human

UniProtKB: P17858

Emily Dimmer

GOA

Human

UniProtKB:P17858

Ruth Lovering

BHF-UCL

Human

UniProtKB:P17858

Varsha Khodiyar

BHF-UCL

Human

UniProtKB:P17858

Ranjana Kishore

WormBase

C. elegans

Worked on PKFL ortholog Y71H10A.1=WBGene00022199

Petra Fey

dictyBase

D. discoideum

DDB_G0274111

Eurie Hong

SGD

S. cerevisiae

SGD:S000003472 (PFK1); SGD:S000004818 (PFK2)

Debby Siegele

ecoliwiki

E. coli

UniProt:P0A796

Brenley McIntosh

ecoliwiki

E. coli

UniProt:P0A796

Jim Hu

ecoliwiki

E. coli

UniProt:P0A796

general wiki maintenance

Tanya Berardini

TAIR

A. thaliana

Arabidopsis PFKL genes, no NEDD4 gene

Li Ni

MGI

Mouse

UniProtKB:P12382

edit table

PFKL

CategoryIDTermHumanMouseRatChickenZfishFlyWormDictyDicotYeastPombeEcoli
Biological ProcessGO:0040018positive regulation of multicellular organism growthXXXXXXIMPXXXXX
Biological ProcessGO:0006096glycolysisIDAIDAXXXICXXIDA ISSIMP IDAXIDA
Biological ProcessGO:0006002fructose 6-phosphate metabolic processIDA IMPXXXXIMPXIDAXXXX
Biological ProcessGO:0031115negative regulation of microtubule polymerizationXXXXXXXIDAXXXX
Biological ProcessGO:0006007glucose catabolic processXXXXXXXIGIXXXIMP
Biological ProcessGO:0009792embryonic development ending in birth or egg hatchingXXXXXXIMPXXXXX
Biological ProcessGO:0000003reproductionXXXXXXIMPXXXXX
Biological ProcessGO:0044275cellular carbohydrate catabolic processXXXXXXXXXXXIMP
Biological ProcessGO:0016052carbohydrate catabolic processXXXXXXXXXXXIMP
Biological ProcessGO:0046676negative regulation of insulin secretionXIDAXXXXXXXXXX
Biological ProcessGO:0009749response to glucose stimulusXIDAXXXXXXXXXX
Molecular FunctionGO:00038726-phosphofructokinase activityIDA IMPIDAXXXIMPXIDA IGIIDA ISSIMPXIMP
Molecular FunctionGO:0015631tubulin bindingXXXXXXXIPIXXXX
Molecular FunctionGO:0005524ATP bindingIDAXXXXXXXXXXIMP
Molecular FunctionGO:0042802identical protein bindingIPIXXXXXXXXXXIDA
Molecular FunctionGO:0005515protein bindingIPIXXXXXXXXXXX
Molecular FunctionGO:0070061fructose bindingIDA ICXXXXXXXXXXX
Molecular FunctionGO:0005488bindingXXXXXXXXXXXIDA
Molecular FunctionGO:0000287magnesium ion bindingXXXXXXXXXXXIDA
Molecular FunctionGO:0032553ribonucleotide bindingXXXXXXXXXXXIDA
Molecular FunctionGO:0043531ADP bindingXXXXXXXXXXXIDA
Cellular ComponentGO:00059456-phosphofructokinase complexIDAXXXXICXIDAXIMPXIDA
Cellular ComponentGO:0005829cytosolIDAIDAXXXXXIDAIDAXXX
Cellular ComponentGO:0005737cytoplasmXXXXXXXXXXXIDA
Cellular ComponentGO:0005886plasma membraneXXXXXXXXIDAXXX
Cellular ComponentGO:0009507chloroplastXXXXXXXXIDAXXX

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GroupOrganismgeneQualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

WormBase

C.elegans

PFKL = C50F4.2 = WBGene0008230

GO:0040018

positive regulation of multicellular organism growth

PMID:11231151[1]

IMP: Inferred from Mutant Phenotype

WB:WBRNAi00002413

P

This annotation is from a large-scale, high-throughput RNAi screen.

complete

FlyBase

Drosophila

FBgn0003071

GO:0003872

6-phosphofructokinase activity

PMID:7929140[2]

IMP: Inferred from Mutant Phenotype

F

complete

FlyBase

Drosophila

FBgn0003071

GO:0005945

6-phosphofructokinase complex

PMID:7929140[2]

IC: Inferred by Curator

GO:0003872

C

complete

FlyBase

Drosophila

FBgn0003071

GO:0006096

glycolysis

PMID:7929140[2]

IC: Inferred by Curator

GO:0003872

P

complete

DictyBase

Dicty

DDB_G0274111

GO:0003872

6-phosphofructokinase activity

PMID:4300706[3] PMID:7813455[4]

IDA: Inferred from Direct Assay

F

purified enzyme

complete

DictyBase

Dicty

DDB_G0274111

GO:0003872

6-phosphofructokinase activity

PMID:7589492[5]

IGI: Inferred from Genetic Interaction

S000003472|S000004818

F

the Dicty recombinant protein expressed in the yeast mutant; yeast has 2 subunits, while Dicty has only one

complete

DictyBase

Dicty

DDB_G0274111

GO:0015631

tubulin binding

PMID:10026266[6]

IPI: Inferred from Physical Interaction

P81948

F

complete

DictyBase

Dicty

DDB_G0274111

GO:0006002

fructose 6-phosphate metabolic process

PMID:7813455[4]

IDA: Inferred from Direct Assay

P

complete

DictyBase

Dicty

DDB_G0274111

GO:0031115

negative regulation of microtubule polymerization

PMID:10026266[6]

IDA: Inferred from Direct Assay

P

complete

DictyBase

Dicty

DDB_G0274111

GO:0006007

glucose catabolic process

PMID:7589492[5]

IGI: Inferred from Genetic Interaction

S000003472|S000004818

P

recombinant Dicty PfkA rescued the glucose growth defect in yeast mutants

complete

DictyBase

Dicty

DDB_G0274111

GO:0005829

cytosol

PMID:7813455[4]

IDA: Inferred from Direct Assay

C

complete

DictyBase

Dicty

DDB_G0274111

GO:0005945

6-phosphofructokinase complex

PMID:7813455[4]

IDA: Inferred from Direct Assay

C

gelfiltration, authors conclude it's a homotetramer

complete

GOA

Human

P17858

GO:0006002

fructose 6-phosphate metabolic process

PMID:6444721[7]

IDA: Inferred from Direct Assay

P

complete

GOA

Human

P17858

GO:0006002

fructose 6-phosphate metabolic process

PMID:6227635[8]

IMP: Inferred from Mutant Phenotype

P

complete

GOA

Human

P17858

GO:0006096

glycolysis

PMID:6444532[9]

IDA:Inferred from Direct Assay

P

complete

GOA

Human

P17858

GO:0006096

glycolysis

PMID:6227635[8]

IDA:Inferred from Direct Assay

P

complete

GOA

Human

P17858

GO:0003872

6-phosphofructokinase activity

PMID:6444721[7]

IDA:Inferred from Direct Assay

F

complete

GOA

Human

P17858

GO:0003872

6-phosphofructokinase activity

PMID:6227635[8]

IMP:Inferred from Mutant Phenotype

F

complete

GOA

Human

P17858

GO:0003872

6-phosphofructokinase activity

PMID:8780720[10]

IDA:Inferred from Direct Assay

F

complete

GOA

Human

P17858

GO:0005524

ATP binding

PMID:8780720[10]

IDA:Inferred from Direct Assay

F

complete

GOA

Human

P17858

GO:0005945

6-phosphofructokinase complex

PMID:6444721[7]

IDA:Inferred from Direct Assay

C

complete

GOA

Human

P17858

GO:0005829

cytosol

PMID:16780588[11]

IDA:Inferred from Direct Assay

C

complete

BHF-UCL

Human

P17858

GO:0042802

identical protein binding

PMID:6444721[7]

IPI: Inferred from Physical Interaction

P17858

F

complete

BHF-UCL

Human

P17858

GO:0005515

protein binding

PMID:6444721[7]

IPI: Inferred from Physical Interaction

P08237

F

complete

BHF-UCL

Human

P17858

GO:0070061

fructose binding

PMID:8780720[10]

IDA: Inferred from Direct Assay

F

complete

BHF-UCL

Human

P17858

GO:0070061

fructose binding

PMID:6444721[7]

IC: Inferred by Curator

GO:0003872

F

complete

WormBase

C.elegans

WBGene00022199

GO:0009792

embryonic development ending in birth or egg hatching

PMID:15791247[12]

IMP: Inferred from Mutant Phenotype

WBRNAi00058226

P

This annotation is from a large-scale, high-throughput RNAi screen.

complete

BHF-UCL

Human

P17858

GO:0005515

protein binding

PMID:6444721[7]

IPI: Inferred from Physical Interaction

P08237

F

complete

WormBase

C.elegans

WBGene00022199

GO:0009792

embryonic development ending in birth or egg hatching

PMID:11231151[1]

IMP: Inferred from Mutant Phenotype

WBRNAi00001724

P

This annotation is from a large-scale, high-throughput RNAi screen.

complete

WormBase

C.elegans

PFKL = C50F4.2 = WBGene0008230

GO:0000003

reproduction

PMID:11231151[1]

IMP: Inferred from Mutant Phenotype

WB:WBRNAi00002413

P

This annotation is from a large-scale, high-throughput RNAi screen.

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0003872

6-phosphofructokinase activity

PMID:125265[13]

IMP: Inferred from Mutant Phenotype

F

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0005488

binding

PMID:17307338[14]

IDA: Inferred from Direct Assay

CHEBI:18021

F

Phosphoenolpyruvate binding is inhibitory to phosphofructokinase activity.

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0005524

ATP binding

PMID:8202475[15]

IMP: Inferred from Mutant Phenotype

F

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0000287

magnesium ion binding

PMID:1445885[16]

IDA: Inferred from Direct Assay

F

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0005945

6-phosphofructokinase complex

PMID:6232272[17]

IDA: Inferred from Direct Assay

C

The E. coli enzyme is a homotetramer

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0032553

ribonucleotide binding

PMID:4229913[18]

IDA: Inferred from Direct Assay

F

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0005737

cytoplasm

PMID:4229913[18]

IDA: Inferred from Direct Assay

C

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0042802

identical protein binding

PMID:11946283[19]

IDA: Inferred from Direct Assay

F

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0044275

cellular carbohydrate catabolic process

PMID:4299078[20]

IMP: Inferred from Mutant Phenotype

P

pfkA mutants are defective in utilization of glucose and mannitol.

complete

SGD

S. cerevisiae

SGD:S000003472 (PFK1)

GO:0003872

6-phosphofructokinase activity

PMID:3007939[21]

IMP: Inferred from Mutant Phenotype

F

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0016052

carbohydrate catabolic process

PMID:4299078[20]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc 11.1[22]. pfk mutants are defective for growth on glucose and mannitol.

complete

SGD

S. cerevisiae

SGD:S000004818 (PFK2)

GO:0003872

6-phosphofructokinase activity

PMID:3007939[21]

IMP: Inferred from Mutant Phenotype

F

complete

SGD

S. cerevisiae

SGD:S000004818 (PFK2)

GO:0006096

glycolysis

PMID:3007939[21]

IMP: Inferred from Mutant Phenotype

P

complete

SGD

S. cerevisiae

SGD:S000003472 (PFK1)

GO:0006096

glycolysis

PMID:3007939[21]

IMP: Inferred from Mutant Phenotype

P

complete

SGD

S. cerevisiae

SGD:S000003472 (PFK1)

GO:0006096

glycolysis

PMID:3000145[23]

IDA: Inferred from Direct Assay

P

complete

SGD

S. cerevisiae

SGD:S000004818 (PFK2)

GO:0006096

glycolysis

PMID:3000145[23]

IDA: Inferred from Direct Assay

P

complete

SGD

S. cerevisiae

SGD:S000004818 (PFK2)

GO:0005945

6-phosphofructokinase complex

PMID:3007939[21]

IMP: Inferred from Mutant Phenotype

C

complete

SGD

S. cerevisiae

SGD:S000003472 (PFK1)

GO:0005945

6-phosphofructokinase complex

PMID:3007939[21]

IMP: Inferred from Mutant Phenotype

C

complete

TAIR

A. thaliana

PFK1 = AT4G29220

GO:0003872

6-phosphofructokinase activity

PMID:17485088[24]

IDA

F

complete

TAIR

A. thaliana

PFK1 = AT4G29220

GO:0006096

glycolysis

PMID:17485088[24]

IDA

P

complete

TAIR

A. thaliana

PFK1 = AT4G29220

GO:0005886

plasma membrane

PMID:17485088[24]

IDA

C

complete

TAIR

A. thaliana

PFK1 = AT4G29220

GO:0005829

cytosol

PMID:17485088[24]

IDA

C

complete

TAIR

A. thaliana

PFK4 = AT5G61580

GO:0003872

6-phosphofructokinase activity

PMID:17485088[24]

IDA

F

complete

TAIR

A. thaliana

PFK4 = AT5G61580

GO:0006096

glycolysis

PMID:17485088[24]

IDA

P

complete

TAIR

A. thaliana

PFK4 = AT5G61580

GO:0009507

chloroplast

PMID:17485088[24]

IDA

C

complete

TAIR

A. thaliana

PFK2 = AT5G47810

GO:0003872

6-phosphofructokinase activity

PMID:17485088[24]

ISS

AGI_LocusCode:AT4G29220

F

complete

TAIR

A. thaliana

PFK2 = AT5G47810

GO:0006096

glycolysis

PMID:17485088[24]

ISS

AGI_LocusCode:AT4G29220

P

complete

TAIR

A. thaliana

PFK2 = AT5G47810

GO:0005829

cytosol

PMID:17485088[24]

IDA

C

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0043531

ADP binding

PMID:11300795[25]

IDA: Inferred from Direct Assay

F

ADP binds the allosteric site of E. coli PfkA

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0006096

glycolysis

PMID:15237399[26]

IDA: Inferred from Direct Assay

P

Reconstitution

complete

FlyBase

Drosophila

FBgn0003071

GO:0006002

fructose 6-phosphate metabolic process

PMID:7929140[2]

IMP: Inferred from Mutant Phenotype

P

complete

MGI

Mouse

Pfkl

GO:0003872

6-phosphofructokinase activity

PMID:8172601[27] PMID:9287040[28]

IDA: Inferred from Direct Assay

F

complete

MGI

Mouse

Pfkl

GO:0005829

cytosol

PMID:2521854[29]

IDA: Inferred from Direct Assay

C

complete

MGI

Mouse

Pfkl

GO:0006096

glycolysis

PMID:8172601[27] PMID:9287040[28]

IDA: Inferred from Direct Assay

P

complete

MGI

Mouse

Pfkl

GO:0046676

negative regulation of insulin secretion

PMID:9287040[28]

IDA: Inferred from Direct Assay

P

complete

MGI

Mouse

Pfkl

GO:0009749

response to glucose stimulus

PMID:9287040[28]

IDA: Inferred from Direct Assay

P

complete

EcoliWiki

E. coli

UniProt:P0A796

GO:0006007

glucose catabolic process

PMID:4299078[20]

IMP: Inferred from Mutant Phenotype

P

complete

edit table

Notes

[back to top]


The October 2008 electronic jamboree also annotated NEDD4

1. Inconsistency of annotations to Fructose 6-P metaoblism. Should all groups have annotated to this if there is an assay for PFK

2. inter-ontology link between F6P metabolism and PKF activity?

3. links between glycolysis and F6P metabolism possible?

4. Annotation to Glycolysis: when can you annotate this process with IDA/IMP to PFKL?

5. EcoliWiki couldn't find GO terms to indicate that the activity PfkA is allosterically regulated. We used GO:0005488 binding for binding of the allosteric effect phosphoenolpyruvate (PEP), which doesn't seem satisfactory. I don't think we need a term for PEP binding, though. I think a more general term for indicate allosteric regulation is what is needed.

6. Sorry for being dense, but what is the difference between GO:0016052 carbohydrate catabolic process and GO:0044275 cellular carbohydrate catabolic process?

References

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See Help:References for how to manage references in GONUTS.

  1. 1.0 1.1 1.2 Maeda I et al. (2001) Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr Biol 11: 171-6 PubMed GONUTS page
  2. 2.0 2.1 2.2 2.3 Currie PD & Sullivan DT (1994) Structure and expression of the gene encoding phosphofructokinase (PFK) in Drosophila melanogaster. J Biol Chem 269: 24679-87 PubMed GONUTS page
  3. Baumann P & Wright BE (1968) The phosphofructokinase of Dictyostelium discoideum. Biochemistry 7: 3653-61 PubMed GONUTS page
  4. 4.0 4.1 4.2 4.3 Martínez-Costa OH et al. (1994) Purification and properties of phosphofructokinase from Dictyostelium discoideum. Eur J Biochem 226: 1007-17 PubMed GONUTS page
  5. 5.0 5.1 Estévez AM et al. (1995) Functional complementation of yeast phosphofructokinase mutants by the non-allosteric enzyme from Dictyostelium discoideum. FEBS Lett 374: 100-4 PubMed GONUTS page
  6. 6.0 6.1 Orosz F et al. (1999) Phosphofructokinase from Dictyostelium discoideum is a potent inhibitor of tubulin polymerization. Biochemistry 38: 1857-65 PubMed GONUTS page
  7. 7.0 7.1 7.2 7.3 7.4 7.5 7.6 Vora S et al. (1980) Isozymes of human phosphofructokinase: identification and subunit structural characterization of a new system. Proc Natl Acad Sci U S A 77: 62-6 PubMed GONUTS page
  8. 8.0 8.1 8.2 Vora S et al. (1983) Heterogeneity of the molecular lesions in inherited phosphofructokinase deficiency. J Clin Invest 72: 1995-2006 PubMed GONUTS page
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  10. 10.0 10.1 10.2 Durante P et al. (1996) Isozyme analysis of human polymorphonuclear leukocyte phosphofructokinase from insulin resistant individuals. Biochem Biophys Res Commun 225: 975-82 PubMed GONUTS page
  11. Hu YH et al. (2006) Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins. BMC Genomics 7: 155 PubMed GONUTS page
  12. Sonnichsen B et al. (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434: 462-9 PubMed GONUTS page
  13. Vinopal RT et al. (1975) PfkA locus of Escherichia coli. J Bacteriol 122: 1162-71 PubMed GONUTS page
  14. Ogawa T et al. (2007) Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli. Res Microbiol 158: 159-63 PubMed GONUTS page
  15. Auzat I et al. (1994) The cooperativity and allosteric inhibition of Escherichia coli phosphofructokinase depend on the interaction between threonine-125 and ATP. Proc Natl Acad Sci U S A 91: 5242-6 PubMed GONUTS page
  16. Johnson JL & Reinhart GD (1992) MgATP and fructose 6-phosphate interactions with phosphofructokinase from Escherichia coli. Biochemistry 31: 11510-8 PubMed GONUTS page
  17. Martel A & Garel JR (1984) Renaturation of the allosteric phosphofructokinase from Escherichia coli. J Biol Chem 259: 4917-21 PubMed GONUTS page
  18. 18.0 18.1 Blangy D et al. (1968) Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli. J Mol Biol 31: 13-35 PubMed GONUTS page
  19. Blangy D (1968) Phosphofructokinase from E. Coli: Evidence for a tetrameric structure of the enzyme. FEBS Lett 2: 109-111 PubMed GONUTS page
  20. 20.0 20.1 20.2 Morrissey AT & Fraenkel DG (1968) Selection of fructose 6-phosphate kinase mutants in Escherichia coli. Biochem Biophys Res Commun 32: 467-73 PubMed GONUTS page
  21. 21.0 21.1 21.2 21.3 21.4 21.5 Heinisch J (1986) Isolation and characterization of the two structural genes coding for phosphofructokinase in yeast. Mol Gen Genet 202: 75-82 PubMed GONUTS page
  22. 23.0 23.1 Hofmann E et al. (1985) Temporal organization of the phosphofructokinase/fructose-1,6-biphosphatase cycle. Adv Enzyme Regul 23: 331-62 PubMed GONUTS page
  23. 24.0 24.1 24.2 24.3 24.4 24.5 24.6 24.7 24.8 24.9 Mustroph A et al. (2007) Characterisation of the ATP-dependent phosphofructokinase gene family from Arabidopsis thaliana. FEBS Lett 581: 2401-10 PubMed GONUTS page
  24. Pham AS et al. (2001) Persistent binding of MgADP to the E187A mutant of Escherichia coli phosphofructokinase in the absence of allosteric effects. Biochemistry 40: 4140-9 PubMed GONUTS page
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  27. 28.0 28.1 28.2 28.3 Knobler H et al. (1997) Impaired glucose-induced insulin response in transgenic mice overexpressing the L-phosphofructokinase gene. Diabetes 46: 1414-8 PubMed GONUTS page
  28. Gekakis N et al. (1989) Phosphofructokinase isozyme expression during myoblast differentiation. J Biol Chem 264: 3658-61 PubMed GONUTS page