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Protein

ATP-dependent 6-phosphofructokinase subunit alpha

Gene

PFK1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis.UniRule annotation8 Publications

Catalytic activityi

ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotationBy similarity

Enzyme regulationi

Allosterically activated by ADP, AMP, or fructose 2,6-bisphosphate, and allosterically inhibited by ATP or citrate.UniRule annotation3 Publications

Kineticsi

  1. KM=0.24 mM for ATP (without effector)1 Publication
  2. KM=0.3 mM for ATP (with 1 mM AMP)1 Publication
  3. KM=0.31 mM for ATP (with 20 µM fructose 2,6-bisphosphate)1 Publication
  4. KM=1.65 mM for fructose 6-phosphate (without effector)1 Publication
  5. KM=0.51 mM for fructose 6-phosphate (with 1 mM AMP)1 Publication
  6. KM=0.11 mM for fructose 6-phosphate (with 20 µM fructose 2,6-bisphosphate)1 Publication

    Pathwayi: glycolysis

    This protein is involved in step 3 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose.UniRule annotation
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. Glucose-6-phosphate isomerase (PGI1)
    3. ATP-dependent 6-phosphofructokinase subunit beta (PFK2), ATP-dependent 6-phosphofructokinase subunit alpha (PFK1)
    4. Fructose-bisphosphate aldolase (FBA1)
    This subpathway is part of the pathway glycolysis, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and glycerone phosphate from D-glucose, the pathway glycolysis and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei215ATP; via amide nitrogenUniRule annotationBy similarity1
    Metal bindingi309Magnesium; catalyticUniRule annotationBy similarity1
    Active sitei356Proton acceptorUniRule annotationBy similarity1
    Binding sitei391Substrate; shared with subunit beta1 Publication1
    Binding sitei455Substrate1 Publication1
    Binding sitei482Substrate; shared with subunit beta1 Publication1
    Binding sitei665Allosteric activator fructose 2,6-bisphosphateUniRule annotation1 Publication1
    Binding sitei760Allosteric activator fructose 2,6-bisphosphate; shared with subunit betaUniRule annotation1 Publication1
    Binding sitei827Allosteric activator fructose 2,6-bisphosphateUniRule annotation1 Publication1
    Binding sitei853Allosteric activator fructose 2,6-bisphosphate; shared with subunit betaUniRule annotation1 Publication1
    Binding sitei952Allosteric activator fructose 2,6-bisphosphateUniRule annotation1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi278 – 279ATPUniRule annotationBy similarity2
    Nucleotide bindingi308 – 311ATPUniRule annotationBy similarity4

    GO - Molecular functioni

    • 6-phosphofructokinase activity Source: SGD
    • ATP binding Source: UniProtKB-KW
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    • fructose 6-phosphate metabolic process Source: InterPro
    • glycolytic process Source: SGD
    • hydrogen ion transmembrane transport Source: GOC
    • proton transport Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Glycolysis

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:YGR240C-MONOMER.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.
    R-SCE-70171. Glycolysis.
    SABIO-RKP16861.
    UniPathwayiUPA00109; UER00182.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent 6-phosphofructokinase subunit alphaUniRule annotation (EC:2.7.1.11UniRule annotation)
    Alternative name(s):
    ATP-dependent 6-phosphofructokinaseUniRule annotation
    Short name:
    ATP-PFKUniRule annotation
    Short name:
    Phosphofructokinase 1UniRule annotation
    PhosphohexokinaseUniRule annotation
    Gene namesi
    Name:PFK1
    Ordered Locus Names:YGR240C
    ORF Names:G8599
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome VII

    Organism-specific databases

    EuPathDBiFungiDB:YGR240C.
    SGDiS000003472. PFK1.

    Subcellular locationi

    GO - Cellular componenti

    • 6-phosphofructokinase complex Source: SGD
    • mitochondrial outer membrane Source: UniProtKB-SubCell
    • mitochondrion Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Membrane, Mitochondrion, Mitochondrion outer membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi309D → T: Reduces maximal activity of the holoenzyme by 50%. Completely abolishes catalytic activity; when associated with 'S-348' in subunit beta. 1 Publication1
    Mutagenesisi356D → S: Reduces maximal activity of the holoenzyme by 50%. Completely abolishes catalytic activity; when associated with 'S-348' in subunit beta. 1 Publication1
    Mutagenesisi447R → S: Reduces maximal activity of the holoenzyme by less than 25%. 1 Publication1
    Mutagenesisi488H → S: Increases the KM for fructose 6-phosphate 20 fold. 1 Publication1
    Mutagenesisi724S → D: Abolishes sensitivity of the holoenzyme to fructose 2,6-bisphosphate activation; when associated with 'D-718' in subunit beta. 1 Publication1
    Mutagenesisi728P → L: Drastically reduces sensitivity of the holoenzyme to ATP inhibition. 1 Publication1
    Mutagenesisi859H → S: Reduces sensitivity of the holoenzyme to fructose 2,6-bisphosphate activation; when associated with 'S-853' in subunit beta. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001120451 – 987ATP-dependent 6-phosphofructokinase subunit alphaAdd BLAST987

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei3PhosphoserineCombined sources1
    Cross-linki89Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei166PhosphoserineCombined sources1
    Modified residuei179PhosphoserineCombined sources1
    Modified residuei185PhosphoserineCombined sources1
    Modified residuei189PhosphoserineCombined sources1
    Modified residuei192PhosphoserineCombined sources1
    Modified residuei217PhosphoserineCombined sources1
    Modified residuei450PhosphothreonineCombined sources1
    Cross-linki625Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP16861.
    PRIDEiP16861.

    PTM databases

    iPTMnetiP16861.

    Interactioni

    Subunit structurei

    Heterooctamer of 4 alpha and 4 beta chains.UniRule annotation3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PFK2P168624EBI-9428,EBI-9435

    Protein-protein interaction databases

    BioGridi33492. 226 interactors.
    DIPiDIP-1505N.
    IntActiP16861. 46 interactors.
    MINTiMINT-393741.

    Structurei

    Secondary structure

    1987
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi207 – 215Combined sources9
    Helixi220 – 233Combined sources14
    Beta strandi237 – 241Combined sources5
    Helixi244 – 250Combined sources7
    Beta strandi254 – 257Combined sources4
    Helixi260 – 263Combined sources4
    Helixi266 – 268Combined sources3
    Helixi281 – 283Combined sources3
    Helixi285 – 297Combined sources13
    Beta strandi300 – 307Combined sources8
    Helixi309 – 319Combined sources11
    Helixi322 – 330Combined sources9
    Beta strandi331 – 334Combined sources4
    Turni337 – 343Combined sources7
    Beta strandi347 – 356Combined sources10
    Helixi368 – 388Combined sources21
    Beta strandi392 – 397Combined sources6
    Helixi404 – 412Combined sources9
    Beta strandi416 – 419Combined sources4
    Helixi421 – 423Combined sources3
    Turni427 – 429Combined sources3
    Helixi430 – 443Combined sources14
    Beta strandi449 – 454Combined sources6
    Helixi467 – 477Combined sources11
    Beta strandi481 – 485Combined sources5
    Helixi487 – 490Combined sources4
    Helixi497 – 515Combined sources19
    Beta strandi524 – 537Combined sources14
    Helixi538 – 553Combined sources16
    Helixi557 – 562Combined sources6
    Helixi568 – 579Combined sources12
    Beta strandi595 – 603Combined sources9
    Helixi608 – 622Combined sources15
    Beta strandi625 – 629Combined sources5
    Helixi632 – 639Combined sources8
    Beta strandi642 – 644Combined sources3
    Turni647 – 652Combined sources6
    Helixi653 – 655Combined sources3
    Helixi668 – 670Combined sources3
    Helixi672 – 681Combined sources10
    Beta strandi685 – 692Combined sources8
    Helixi693 – 705Combined sources13
    Turni706 – 708Combined sources3
    Helixi710 – 713Combined sources4
    Beta strandi716 – 721Combined sources6
    Helixi736 – 757Combined sources22
    Beta strandi758 – 766Combined sources9
    Helixi773 – 780Combined sources8
    Turni781 – 783Combined sources3
    Beta strandi785 – 788Combined sources4
    Beta strandi790 – 792Combined sources3
    Helixi796 – 812Combined sources17
    Beta strandi821 – 826Combined sources6
    Beta strandi831 – 833Combined sources3
    Helixi835 – 846Combined sources12
    Beta strandi849 – 856Combined sources8
    Helixi858 – 862Combined sources5
    Helixi868 – 890Combined sources23
    Helixi921 – 923Combined sources3
    Beta strandi924 – 930Combined sources7
    Beta strandi933 – 938Combined sources6
    Helixi939 – 942Combined sources4
    Turni948 – 951Combined sources4
    Beta strandi953 – 955Combined sources3
    Helixi960 – 969Combined sources10
    Helixi972 – 978Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3O8OX-ray2.90A/C/E/G201-987[»]
    ProteinModelPortaliP16861.
    SMRiP16861.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni1 – 580N-terminal catalytic PFK domain 1UniRule annotation1 PublicationAdd BLAST580
    Regioni354 – 356Substrate bindingUniRule annotation1 Publication3
    Regioni398 – 400Substrate bindingUniRule annotation1 Publication3
    Regioni488 – 491Substrate bindingUniRule annotation1 Publication4
    Regioni581 – 594Interdomain linkerUniRule annotation1 PublicationAdd BLAST14
    Regioni595 – 987C-terminal regulatory PFK domain 2UniRule annotation1 PublicationAdd BLAST393
    Regioni722 – 726Allosteric activator fructose 2,6-bisphosphate bindingUniRule annotation1 Publication5
    Regioni767 – 769Allosteric activator fructose 2,6-bisphosphate bindingUniRule annotation1 Publication3
    Regioni859 – 862Allosteric activator fructose 2,6-bisphosphate bindingUniRule annotation1 Publication4

    Sequence similaritiesi

    Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Eukaryotic two domain clade "E" sub-subfamily.UniRule annotation

    Phylogenomic databases

    GeneTreeiENSGT00390000013209.
    HOGENOMiHOG000200154.
    InParanoidiP16861.
    KOiK00850.
    OMAiEVYAIYE.
    OrthoDBiEOG092C0LOE.

    Family and domain databases

    HAMAPiMF_03184. Phosphofructokinase_I_E. 1 hit.
    InterProiIPR009161. 6-Pfructokinase_euk.
    IPR022953. ATP_PFK.
    IPR015912. Phosphofructokinase_CS.
    IPR000023. Phosphofructokinase_dom.
    [Graphical view]
    PfamiPF00365. PFK. 2 hits.
    [Graphical view]
    PIRSFiPIRSF000533. ATP_PFK_euk. 1 hit.
    PRINTSiPR00476. PHFRCTKINASE.
    SUPFAMiSSF53784. SSF53784. 3 hits.
    TIGRFAMsiTIGR02478. 6PF1K_euk. 1 hit.
    PROSITEiPS00433. PHOSPHOFRUCTOKINASE. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P16861-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQSQDSCYGV AFRSIITNDE ALFKKTIHFY HTLGFATVKD FNKFKHGENS
    60 70 80 90 100
    LLSSGTSQDS LREVWLESFK LSEVDASGFR IPQQEATNKA QSQGALLKIR
    110 120 130 140 150
    LVMSAPIDET FDTNETATIT YFSTDLNKIV EKFPKQAEKL SDTLVFLKDP
    160 170 180 190 200
    MGNNITFSGL ANATDSAPTS KDAFLEATSE DEIISRASSD ASDLLRQTLG
    210 220 230 240 250
    SSQKKKKIAV MTSGGDSPGM NAAVRAVVRT GIHFGCDVFA VYEGYEGLLR
    260 270 280 290 300
    GGKYLKKMAW EDVRGWLSEG GTLIGTARSM EFRKREGRRQ AAGNLISQGI
    310 320 330 340 350
    DALVVCGGDG SLTGADLFRH EWPSLVDELV AEGRFTKEEV APYKNLSIVG
    360 370 380 390 400
    LVGSIDNDMS GTDSTIGAYS ALERICEMVD YIDATAKSHS RAFVVEVMGR
    410 420 430 440 450
    HCGWLALMAG IATGADYIFI PERAVPHGKW QDELKEVCQR HRSKGRRNNT
    460 470 480 490 500
    IIVAEGALDD QLNPVTANDV KDALIELGLD TKVTILGHVQ RGGTAVAHDR
    510 520 530 540 550
    WLATLQGVDA VKAVLEFTPE TPSPLIGILE NKIIRMPLVE SVKLTKSVAT
    560 570 580 590 600
    AIENKDFDKA ISLRDTEFIE LYENFLSTTV KDDGSELLPV SDRLNIGIVH
    610 620 630 640 650
    VGAPSAALNA ATRAATLYCL SHGHKPYAIM NGFSGLIQTG EVKELSWIDV
    660 670 680 690 700
    ENWHNLGGSE IGTNRSVASE DLGTIAYYFQ KNKLDGLIIL GGFEGFRSLK
    710 720 730 740 750
    QLRDGRTQHP IFNIPMCLIP ATVSNNVPGT EYSLGVDTCL NALVNYTDDI
    760 770 780 790 800
    KQSASATRRR VFVCEVQGGH SGYIASFTGL ITGAVSVYTP EKKIDLASIR
    810 820 830 840 850
    EDITLLKENF RHDKGENRNG KLLVRNEQAS SVYSTQLLAD IISEASKGKF
    860 870 880 890 900
    GVRTAIPGHV QQGGVPSSKD RVTASRFAVK CIKFIEQWNK KNEASPNTDA
    910 920 930 940 950
    KVLRFKFDTH GEKVPTVEHE DDSAAVICVN GSHVSFKPIA NLWENETNVE
    960 970 980
    LRKGFEVHWA EYNKIGDILS GRLKLRAEVA ALAAENK
    Length:987
    Mass (Da):107,970
    Last modified:August 1, 1990 - v1
    Checksum:i995B3DF7C7781B29
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M26943 Genomic DNA. Translation: AAA34859.1.
    Z73025 Genomic DNA. Translation: CAA97268.1.
    X87941 Genomic DNA. Translation: CAA61193.1.
    BK006941 Genomic DNA. Translation: DAA08331.1.
    PIRiJQ0016.
    RefSeqiNP_011756.1. NM_001181369.1.

    Genome annotation databases

    EnsemblFungiiYGR240C; YGR240C; YGR240C.
    GeneIDi853155.
    KEGGisce:YGR240C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M26943 Genomic DNA. Translation: AAA34859.1.
    Z73025 Genomic DNA. Translation: CAA97268.1.
    X87941 Genomic DNA. Translation: CAA61193.1.
    BK006941 Genomic DNA. Translation: DAA08331.1.
    PIRiJQ0016.
    RefSeqiNP_011756.1. NM_001181369.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3O8OX-ray2.90A/C/E/G201-987[»]
    ProteinModelPortaliP16861.
    SMRiP16861.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi33492. 226 interactors.
    DIPiDIP-1505N.
    IntActiP16861. 46 interactors.
    MINTiMINT-393741.

    PTM databases

    iPTMnetiP16861.

    Proteomic databases

    MaxQBiP16861.
    PRIDEiP16861.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYGR240C; YGR240C; YGR240C.
    GeneIDi853155.
    KEGGisce:YGR240C.

    Organism-specific databases

    EuPathDBiFungiDB:YGR240C.
    SGDiS000003472. PFK1.

    Phylogenomic databases

    GeneTreeiENSGT00390000013209.
    HOGENOMiHOG000200154.
    InParanoidiP16861.
    KOiK00850.
    OMAiEVYAIYE.
    OrthoDBiEOG092C0LOE.

    Enzyme and pathway databases

    UniPathwayiUPA00109; UER00182.
    BioCyciYEAST:YGR240C-MONOMER.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.
    R-SCE-70171. Glycolysis.
    SABIO-RKP16861.

    Miscellaneous databases

    PROiP16861.

    Family and domain databases

    HAMAPiMF_03184. Phosphofructokinase_I_E. 1 hit.
    InterProiIPR009161. 6-Pfructokinase_euk.
    IPR022953. ATP_PFK.
    IPR015912. Phosphofructokinase_CS.
    IPR000023. Phosphofructokinase_dom.
    [Graphical view]
    PfamiPF00365. PFK. 2 hits.
    [Graphical view]
    PIRSFiPIRSF000533. ATP_PFK_euk. 1 hit.
    PRINTSiPR00476. PHFRCTKINASE.
    SUPFAMiSSF53784. SSF53784. 3 hits.
    TIGRFAMsiTIGR02478. 6PF1K_euk. 1 hit.
    PROSITEiPS00433. PHOSPHOFRUCTOKINASE. 2 hits.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPFKA1_YEAST
    AccessioniPrimary (citable) accession number: P16861
    Secondary accession number(s): D6VV20
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: August 1, 1990
    Last modified: November 30, 2016
    This is version 158 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 89800 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.