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Protein

ATP-dependent 6-phosphofructokinase

Gene

pfkA

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
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 annotation1 Publication

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 and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate.

Kineticsi

  1. KM=0.07 mM for ATP1 Publication
  2. KM=0.033 mM for fructose 6-phosphate1 Publication

    Pathway: 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 A (pgiA), Glucose-6-phosphate isomerase (GT94_02025), Glucose-6-phosphate isomerase (GT94_17655), Glucose-6-phosphate isomerase B (pgiB)
    3. ATP-dependent 6-phosphofructokinase (pfkA)
    4. Fructose-bisphosphate aldolase (fba)
    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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei11 – 111ATP; via amide nitrogen
    Binding sitei59 – 591Allosteric activator ADP; shared with dimeric partner
    Metal bindingi103 – 1031Magnesium; catalyticUniRule annotation
    Active sitei127 – 1271Proton acceptor
    Binding sitei154 – 1541Allosteric activator ADP
    Binding sitei162 – 1621Substrate; shared with dimeric partner
    Binding sitei211 – 2111Allosteric activator ADP
    Binding sitei222 – 2221Substrate
    Binding sitei243 – 2431Substrate; shared with dimeric partner

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi72 – 732ATP
    Nucleotide bindingi102 – 1054ATP

    GO - Molecular functioni

    GO - Biological processi

    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

    BRENDAi2.7.1.11. 623.
    SABIO-RKP00512.
    UniPathwayiUPA00109; UER00182.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent 6-phosphofructokinaseUniRule annotation (EC:2.7.1.11UniRule annotation)
    Short name:
    ATP-PFKUniRule annotation
    Short name:
    PhosphofructokinaseUniRule annotation
    Alternative name(s):
    PhosphohexokinaseUniRule annotation
    Gene namesi
    Name:pfkAUniRule annotation
    Synonyms:pfk
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 319319ATP-dependent 6-phosphofructokinasePRO_0000111935Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.UniRule annotation4 Publications

    Structurei

    Secondary structure

    1
    319
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 119Combined sources
    Helixi16 – 2914Combined sources
    Beta strandi33 – 375Combined sources
    Helixi40 – 467Combined sources
    Beta strandi49 – 524Combined sources
    Helixi54 – 574Combined sources
    Helixi74 – 774Combined sources
    Helixi81 – 9111Combined sources
    Beta strandi97 – 1026Combined sources
    Helixi103 – 11412Combined sources
    Beta strandi119 – 1279Combined sources
    Helixi139 – 15315Combined sources
    Beta strandi159 – 16810Combined sources
    Helixi175 – 1839Combined sources
    Beta strandi187 – 1904Combined sources
    Helixi198 – 21013Combined sources
    Beta strandi216 – 2216Combined sources
    Turni222 – 2243Combined sources
    Helixi227 – 23812Combined sources
    Beta strandi241 – 2466Combined sources
    Helixi248 – 2525Combined sources
    Helixi258 – 27720Combined sources
    Beta strandi281 – 2877Combined sources
    Beta strandi290 – 2956Combined sources
    Helixi296 – 3005Combined sources
    Helixi308 – 31710Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MTOX-ray3.20A/B/C/D/E/F/G/H1-319[»]
    3PFKX-ray2.40A1-319[»]
    3U39X-ray2.79A/B/C/D1-319[»]
    4I36X-ray2.30A/B/C/D1-319[»]
    4I4IX-ray2.49A/B/C/D1-319[»]
    4I7EX-ray2.00A/B/C/D1-319[»]
    4PFKX-ray2.40A1-319[»]
    6PFKX-ray2.60A/B/C/D1-319[»]
    ProteinModelPortaliP00512.
    SMRiP00512. Positions 1-319.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00512.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni21 – 255Allosteric activator ADP binding; shared with dimeric partner
    Regioni125 – 1273Substrate binding
    Regioni169 – 1713Substrate binding
    Regioni185 – 1873Allosteric activator ADP binding
    Regioni213 – 2153Allosteric activator ADP binding
    Regioni249 – 2524Substrate binding

    Sequence similaritiesi

    Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade "B1" sub-subfamily.UniRule annotation

    Family and domain databases

    HAMAPiMF_00339. Phosphofructokinase_I_B1.
    InterProiIPR022953. ATP_PFK.
    IPR012003. ATP_PFK_prok-type.
    IPR012828. PFKA_ATP_prok.
    IPR015912. Phosphofructokinase_CS.
    IPR000023. Phosphofructokinase_dom.
    [Graphical view]
    PfamiPF00365. PFK. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000532. ATP_PFK_prok. 1 hit.
    PRINTSiPR00476. PHFRCTKINASE.
    SUPFAMiSSF53784. SSF53784. 1 hit.
    TIGRFAMsiTIGR02482. PFKA_ATP. 1 hit.
    PROSITEiPS00433. PHOSPHOFRUCTOKINASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P00512-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKRIGVLTSG GDSPGMNAAI RSVVRKAIYH GVEVYGVYHG YAGLIAGNIK
    60 70 80 90 100
    KLEVGDVGDI IHRGGTILYT ARCPEFKTEE GQKKGIEQLK KHGIEGLVVI
    110 120 130 140 150
    GGDGSYQGAK KLTEHGFPCV GVPGTIDNDI PGTDFTIGFD TALNTVIDAI
    160 170 180 190 200
    DKIRDTATSH ERTYVIEVMG RHAGDIALWS GLAGGAETIL IPEADYDMND
    210 220 230 240 250
    VIARLKRGHE RGKKHSIIIV AEGVGSGVDF GRQIQEATGF ETRVTVLGHV
    260 270 280 290 300
    QRGGSPTAFD RVLASRLGAR AVELLLEGKG GRCVGIQNNQ LVDHDIAEAL
    310
    ANKHTIDQRM YALSKELSI
    Length:319
    Mass (Da):34,119
    Last modified:July 1, 1989 - v2
    Checksum:iEE968D39BA30712B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti12 – 121D → N AA sequence (PubMed:6447595).Curated
    Sequence conflicti35 – 373Missing AA sequence (PubMed:6447595).Curated
    Sequence conflicti43 – 431G → V AA sequence (PubMed:6447595).Curated
    Sequence conflicti82 – 821Q → E AA sequence (PubMed:6447595).Curated
    Sequence conflicti95 – 951E → Q AA sequence (PubMed:6447595).Curated
    Sequence conflicti225 – 2251G → L AA sequence (PubMed:6447595).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M15643 Genomic DNA. Translation: AAA22656.1.
    D13095 Genomic DNA. Translation: BAA02405.1.
    PIRiA27474. KIBSFF.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M15643 Genomic DNA. Translation: AAA22656.1.
    D13095 Genomic DNA. Translation: BAA02405.1.
    PIRiA27474. KIBSFF.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MTOX-ray3.20A/B/C/D/E/F/G/H1-319[»]
    3PFKX-ray2.40A1-319[»]
    3U39X-ray2.79A/B/C/D1-319[»]
    4I36X-ray2.30A/B/C/D1-319[»]
    4I4IX-ray2.49A/B/C/D1-319[»]
    4I7EX-ray2.00A/B/C/D1-319[»]
    4PFKX-ray2.40A1-319[»]
    6PFKX-ray2.60A/B/C/D1-319[»]
    ProteinModelPortaliP00512.
    SMRiP00512. Positions 1-319.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00109; UER00182.
    BRENDAi2.7.1.11. 623.
    SABIO-RKP00512.

    Miscellaneous databases

    EvolutionaryTraceiP00512.

    Family and domain databases

    HAMAPiMF_00339. Phosphofructokinase_I_B1.
    InterProiIPR022953. ATP_PFK.
    IPR012003. ATP_PFK_prok-type.
    IPR012828. PFKA_ATP_prok.
    IPR015912. Phosphofructokinase_CS.
    IPR000023. Phosphofructokinase_dom.
    [Graphical view]
    PfamiPF00365. PFK. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000532. ATP_PFK_prok. 1 hit.
    PRINTSiPR00476. PHFRCTKINASE.
    SUPFAMiSSF53784. SSF53784. 1 hit.
    TIGRFAMsiTIGR02482. PFKA_ATP. 1 hit.
    PROSITEiPS00433. PHOSPHOFRUCTOKINASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Nucleotide sequence of the phosphofructokinase gene from Bacillus stearothermophilus and comparison with the homologous Escherichia coli gene."
      French B.A., Chang S.H.
      Gene 54:65-71(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Phosphofructokinase: complete amino-acid sequence of the enzyme from Bacillus stearothermophilus."
      Kolb E., Hudson P.J., Harris J.I.
      Eur. J. Biochem. 108:587-597(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE.
    3. "Molecular cloning and nucleotide sequence of the gene for pyruvate kinase of Bacillus stearothermophilus and the production of the enzyme in Escherichia coli. Evidence that the genes for phosphofructokinase and pyruvate kinase constitute an operon."
      Sakai H., Ohta T.
      Eur. J. Biochem. 211:851-859(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 300-319.
    4. "Kinetic characteristics of phosphofructokinase from Bacillus stearothermophilus: MgATP nonallosterically inhibits the enzyme."
      Byrnes M., Zhu X., Younathan E.S., Chang S.H.
      Biochemistry 33:3424-3431(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    5. "Structure and control of phosphofructokinase from Bacillus stearothermophilus."
      Evans P.R., Hudson P.J.
      Nature 279:500-504(1979) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
    6. Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH MAGNESIUM; ADP AND FRUCTOSE-6-PHOSPHATE.
    7. "Structural basis of the allosteric behaviour of phosphofructokinase."
      Schirmer T., Evans P.R.
      Nature 343:140-145(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH ALLOSTERIC INHIBITOR.
    8. "Reversible ligand-induced dissociation of a tryptophan-shift mutant of phosphofructokinase from Bacillus stearothermophilus."
      Riley-Lovingshimer M.R., Ronning D.R., Sacchettini J.C., Reinhart G.D.
      Biochemistry 41:12967-12974(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) IN COMPLEX WITH FRUCTOSE-6-PHOSPHATE.
    9. "Structure of the apo form of Bacillus stearothermophilus phosphofructokinase."
      Mosser R., Reddy M.C., Bruning J.B., Sacchettini J.C., Reinhart G.D.
      Biochemistry 51:769-775(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.79 ANGSTROMS).
    10. "Redefining the role of the quaternary shift in Bacillus stearothermophilus phosphofructokinase."
      Mosser R., Reddy M.C., Bruning J.B., Sacchettini J.C., Reinhart G.D.
      Biochemistry 52:5421-5429(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH PHOSPHOENOLPYRUVIC ACID.

    Entry informationi

    Entry nameiPFKA_GEOSE
    AccessioniPrimary (citable) accession number: P00512
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 1, 1989
    Last modified: May 27, 2015
    This is version 129 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    In the R state the 6-P group of fructose 6-phosphate (F6P) is bound by His-249 from one chain and Arg-162 and Arg-243 from an adjacent chain. In the T state a conformation change moves Arg-162 away from the substrate. Glu-161 takes its place, hence repelling the phosphate of ATP.
    The phosphate group of phosphoenolpyruvate appears to bind in the same place as the beta-phosphate group of ADP.

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Direct protein sequencing

    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

    External Data

    Dasty 3

    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 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.