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Protein

ATP-dependent 6-phosphofructokinase subunit beta

Gene

PFK2

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 annotation

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 sitei206ATP; via amide nitrogenUniRule annotation1
    Metal bindingi301Magnesium; catalyticUniRule annotation1
    Active sitei348Proton acceptorUniRule annotation1
    Binding sitei383Substrate; shared with subunit alphaUniRule annotation1 Publication1
    Binding sitei447SubstrateUniRule annotation1 Publication1
    Binding sitei475Substrate; shared with subunit alphaUniRule annotation1 Publication1
    Binding sitei658Allosteric activator fructose 2,6-bisphosphateUniRule annotation1 Publication1
    Binding sitei754Allosteric activator fructose 2,6-bisphosphate; shared with subunit alphaUniRule annotation1
    Binding sitei847Allosteric activator fructose 2,6-bisphosphate; shared with subunit alphaUniRule annotation1
    Binding sitei935Allosteric activator fructose 2,6-bisphosphateUniRule annotation1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi270 – 271ATPUniRule annotation2
    Nucleotide bindingi300 – 303ATPUniRule annotation4

    GO - Molecular functioni

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

    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:YMR205C-MONOMER.
    BRENDAi2.7.1.11. 984.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.
    R-SCE-70171. Glycolysis.
    SABIO-RKP16862.
    UniPathwayiUPA00109; UER00182.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent 6-phosphofructokinase subunit betaUniRule annotation (EC:2.7.1.11UniRule annotation)
    Alternative name(s):
    ATP-dependent 6-phosphofructokinaseUniRule annotation
    Short name:
    ATP-PFKUniRule annotation
    Short name:
    Phosphofructokinase 2UniRule annotation
    PhosphohexokinaseUniRule annotation
    Gene namesi
    Name:PFK2
    Ordered Locus Names:YMR205C
    ORF Names:YM8325.06C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XIII

    Organism-specific databases

    EuPathDBiFungiDB:YMR205C.
    SGDiS000004818. PFK2.

    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
    Mutagenesisi301D → T: Reduces maximal activity of the holoenzyme by 30%. 1 Publication1
    Mutagenesisi348D → S: Reduces maximal activity of the holoenzyme by 50%. Completely abolishes catalytic activity; when associated with 'T-309' or 'S-356' in subunit alpha. 1 Publication1
    Mutagenesisi439R → V: Reduces maximal activity of the holoenzyme by less than 25%. 1 Publication1
    Mutagenesisi481H → S: Increases the KM for fructose 6-phosphate 50 fold. 1 Publication1
    Mutagenesisi718S → D: Abolishes sensitivity of the holoenzyme to fructose 2,6-bisphosphate activation; when associated with 'D-724' in subunit alpha. 1 Publication1
    Mutagenesisi722P → L: Drastically reduces sensitivity of the holoenzyme to ATP inhibition. 1 Publication1
    Mutagenesisi853H → S: Reduces sensitivity of the holoenzyme to fructose 2,6-bisphosphate activation; when associated with 'S-859' in subunit alpha. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001120462 – 959ATP-dependent 6-phosphofructokinase subunit betaAdd BLAST958

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei152PhosphothreonineCombined sources1
    Modified residuei163PhosphoserineCombined sources1
    Modified residuei171PhosphoserineCombined sources1
    Modified residuei803PhosphoserineCombined sources1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP16862.
    PRIDEiP16862.

    PTM databases

    iPTMnetiP16862.

    Interactioni

    Subunit structurei

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

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PFK1P168614EBI-9435,EBI-9428
    RSP5P399403EBI-9435,EBI-16219

    Protein-protein interaction databases

    BioGridi35383. 175 interactors.
    DIPiDIP-2619N.
    IntActiP16862. 44 interactors.
    MINTiMINT-424355.

    Structurei

    Secondary structure

    1959
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi198 – 206Combined sources9
    Helixi211 – 225Combined sources15
    Beta strandi228 – 232Combined sources5
    Helixi235 – 240Combined sources6
    Turni244 – 246Combined sources3
    Beta strandi247 – 250Combined sources4
    Helixi252 – 255Combined sources4
    Helixi258 – 260Combined sources3
    Helixi273 – 275Combined sources3
    Helixi277 – 289Combined sources13
    Beta strandi294 – 299Combined sources6
    Helixi301 – 322Combined sources22
    Beta strandi325 – 327Combined sources3
    Helixi329 – 334Combined sources6
    Beta strandi339 – 345Combined sources7
    Helixi360 – 380Combined sources21
    Beta strandi384 – 389Combined sources6
    Helixi396 – 405Combined sources10
    Beta strandi408 – 411Combined sources4
    Helixi421 – 435Combined sources15
    Beta strandi441 – 446Combined sources6
    Helixi459 – 468Combined sources10
    Beta strandi474 – 478Combined sources5
    Helixi480 – 483Combined sources4
    Helixi490 – 509Combined sources20
    Beta strandi517 – 524Combined sources8
    Beta strandi526 – 530Combined sources5
    Helixi531 – 546Combined sources16
    Helixi550 – 556Combined sources7
    Helixi561 – 573Combined sources13
    Beta strandi581 – 584Combined sources4
    Beta strandi588 – 596Combined sources9
    Helixi601 – 615Combined sources15
    Beta strandi618 – 622Combined sources5
    Helixi625 – 632Combined sources8
    Beta strandi635 – 637Combined sources3
    Helixi640 – 643Combined sources4
    Helixi646 – 648Combined sources3
    Helixi661 – 664Combined sources4
    Helixi666 – 676Combined sources11
    Beta strandi679 – 686Combined sources8
    Helixi687 – 697Combined sources11
    Turni698 – 702Combined sources5
    Helixi704 – 706Combined sources3
    Beta strandi712 – 715Combined sources4
    Helixi730 – 751Combined sources22
    Beta strandi752 – 760Combined sources9
    Helixi767 – 776Combined sources10
    Beta strandi779 – 782Combined sources4
    Turni784 – 786Combined sources3
    Helixi790 – 807Combined sources18
    Beta strandi815 – 820Combined sources6
    Helixi821 – 823Combined sources3
    Helixi829 – 840Combined sources12
    Beta strandi845 – 850Combined sources6
    Helixi852 – 856Combined sources5
    Helixi862 – 881Combined sources20
    Helixi884 – 889Combined sources6
    Beta strandi890 – 894Combined sources5
    Helixi901 – 904Combined sources4
    Beta strandi907 – 911Combined sources5
    Beta strandi913 – 915Combined sources3
    Beta strandi918 – 921Combined sources4
    Helixi922 – 928Combined sources7
    Helixi932 – 934Combined sources3
    Beta strandi935 – 939Combined sources5
    Helixi943 – 952Combined sources10

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3O8OX-ray2.90B/D/F/H194-959[»]
    ProteinModelPortaliP16862.
    SMRiP16862.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni2 – 573N-terminal catalytic PFK domain 1UniRule annotation1 PublicationAdd BLAST572
    Regioni346 – 348Substrate bindingUniRule annotation1 Publication3
    Regioni390 – 392Substrate bindingUniRule annotation1 Publication3
    Regioni481 – 484Substrate bindingUniRule annotation1 Publication4
    Regioni574 – 587Interdomain linkerUniRule annotation1 PublicationAdd BLAST14
    Regioni588 – 959C-terminal regulatory PFK domain 2UniRule annotation1 PublicationAdd BLAST372
    Regioni716 – 720Allosteric activator fructose 2,6-bisphosphate bindingUniRule annotation1 Publication5
    Regioni761 – 763Allosteric activator fructose 2,6-bisphosphate bindingUniRule annotation1 Publication3
    Regioni853 – 856Allosteric 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.
    InParanoidiP16862.
    KOiK00850.
    OMAiGTNRQTP.
    OrthoDBiEOG092C0LOE.

    Family and domain databases

    Gene3Di3.10.180.10. 1 hit.
    HAMAPiMF_03184. Phosphofructokinase_I_E. 1 hit.
    InterProiIPR009161. 6-Pfructokinase_euk.
    IPR022953. ATP_PFK.
    IPR029068. Glyas_Bleomycin-R_OHBP_Dase.
    IPR015912. Phosphofructokinase_CS.
    IPR000023. Phosphofructokinase_dom.
    [Graphical view]
    PfamiPF00365. PFK. 2 hits.
    [Graphical view]
    PIRSFiPIRSF000533. ATP_PFK_euk. 1 hit.
    PRINTSiPR00476. PHFRCTKINASE.
    SUPFAMiSSF53784. SSF53784. 2 hits.
    SSF54593. SSF54593. 1 hit.
    TIGRFAMsiTIGR02478. 6PF1K_euk. 1 hit.
    PROSITEiPS00433. PHOSPHOFRUCTOKINASE. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P16862-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTVTTPFVNG TSYCTVTAYS VQSYKAAIDF YTKFLSLENR SSPDENSTLL
    60 70 80 90 100
    SNDSISLKIL LRPDEKINKN VEAHLKELNS ITKTQDWRSH ATQSLVFNTS
    110 120 130 140 150
    DILAVKDTLN AMNAPLQGYP TELFPMQLYT LDPLGNVVGV TSTKNAVSTK
    160 170 180 190 200
    PTPPPAPEAS AESGLSSKVH SYTDLAYRMK TTDTYPSLPK PLNRPQKAIA
    210 220 230 240 250
    VMTSGGDAPG MNSNVRAIVR SAIFKGCRAF VVMEGYEGLV RGGPEYIKEF
    260 270 280 290 300
    HWEDVRGWSA EGGTNIGTAR CMEFKKREGR LLGAQHLIEA GVDALIVCGG
    310 320 330 340 350
    DGSLTGADLF RSEWPSLIEE LLKTNRISNE QYERMKHLNI CGTVGSIDND
    360 370 380 390 400
    MSTTDATIGA YSALDRICKA IDYVEATANS HSRAFVVEVM GRNCGWLALL
    410 420 430 440 450
    AGIATSADYI FIPEKPATSS EWQDQMCDIV SKHRSRGKRT TIVVVAEGAI
    460 470 480 490 500
    AADLTPISPS DVHKVLVDRL GLDTRITTLG HVQRGGTAVA YDRILATLQG
    510 520 530 540 550
    LEAVNAVLES TPDTPSPLIA VNENKIVRKP LMESVKLTKA VAEAIQAKDF
    560 570 580 590 600
    KRAMSLRDTE FIEHLNNFMA INSADHNEPK LPKDKRLKIA IVNVGAPAGG
    610 620 630 640 650
    INSAVYSMAT YCMSQGHRPY AIYNGWSGLA RHESVRSLNW KDMLGWQSRG
    660 670 680 690 700
    GSEIGTNRVT PEEADLGMIA YYFQKYEFDG LIIVGGFEAF ESLHQLERAR
    710 720 730 740 750
    ESYPAFRIPM VLIPATLSNN VPGTEYSLGS DTALNALMEY CDVVKQSASS
    760 770 780 790 800
    TRGRAFVVDC QGGNSGYLAT YASLAVGAQV SYVPEEGISL EQLSEDIEYL
    810 820 830 840 850
    AQSFEKAEGR GRFGKLILKS TNASKALSAT KLAEVITAEA DGRFDAKPAY
    860 870 880 890 900
    PGHVQQGGLP SPIDRTRATR MAIKAVGFIK DNQAAIAEAR AAEENFNADD
    910 920 930 940 950
    KTISDTAAVV GVKGSHVVYN SIRQLYDYET EVSMRMPKVI HWQATRLIAD

    HLVGRKRVD
    Length:959
    Mass (Da):104,618
    Last modified:January 23, 2007 - v4
    Checksum:i82CE6402CEDBBCB2
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti137V → G in AAA34860 (PubMed:2528496).Curated1
    Sequence conflicti880K → E in AAA34860 (PubMed:2528496).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M26944 Genomic DNA. Translation: AAA34860.1.
    Z48755 Genomic DNA. Translation: CAA88646.1.
    BK006946 Genomic DNA. Translation: DAA10104.1.
    PIRiS59446. JQ0017.
    RefSeqiNP_013932.1. NM_001182712.1.

    Genome annotation databases

    EnsemblFungiiYMR205C; YMR205C; YMR205C.
    GeneIDi855245.
    KEGGisce:YMR205C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M26944 Genomic DNA. Translation: AAA34860.1.
    Z48755 Genomic DNA. Translation: CAA88646.1.
    BK006946 Genomic DNA. Translation: DAA10104.1.
    PIRiS59446. JQ0017.
    RefSeqiNP_013932.1. NM_001182712.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3O8OX-ray2.90B/D/F/H194-959[»]
    ProteinModelPortaliP16862.
    SMRiP16862.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi35383. 175 interactors.
    DIPiDIP-2619N.
    IntActiP16862. 44 interactors.
    MINTiMINT-424355.

    PTM databases

    iPTMnetiP16862.

    Proteomic databases

    MaxQBiP16862.
    PRIDEiP16862.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYMR205C; YMR205C; YMR205C.
    GeneIDi855245.
    KEGGisce:YMR205C.

    Organism-specific databases

    EuPathDBiFungiDB:YMR205C.
    SGDiS000004818. PFK2.

    Phylogenomic databases

    GeneTreeiENSGT00390000013209.
    HOGENOMiHOG000200154.
    InParanoidiP16862.
    KOiK00850.
    OMAiGTNRQTP.
    OrthoDBiEOG092C0LOE.

    Enzyme and pathway databases

    UniPathwayiUPA00109; UER00182.
    BioCyciYEAST:YMR205C-MONOMER.
    BRENDAi2.7.1.11. 984.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.
    R-SCE-70171. Glycolysis.
    SABIO-RKP16862.

    Miscellaneous databases

    PROiP16862.

    Family and domain databases

    Gene3Di3.10.180.10. 1 hit.
    HAMAPiMF_03184. Phosphofructokinase_I_E. 1 hit.
    InterProiIPR009161. 6-Pfructokinase_euk.
    IPR022953. ATP_PFK.
    IPR029068. Glyas_Bleomycin-R_OHBP_Dase.
    IPR015912. Phosphofructokinase_CS.
    IPR000023. Phosphofructokinase_dom.
    [Graphical view]
    PfamiPF00365. PFK. 2 hits.
    [Graphical view]
    PIRSFiPIRSF000533. ATP_PFK_euk. 1 hit.
    PRINTSiPR00476. PHFRCTKINASE.
    SUPFAMiSSF53784. SSF53784. 2 hits.
    SSF54593. SSF54593. 1 hit.
    TIGRFAMsiTIGR02478. 6PF1K_euk. 1 hit.
    PROSITEiPS00433. PHOSPHOFRUCTOKINASE. 2 hits.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPFKA2_YEAST
    AccessioniPrimary (citable) accession number: P16862
    Secondary accession number(s): D6W030
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: January 23, 2007
    Last modified: November 30, 2016
    This is version 169 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 90200 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 XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: 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.