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Protein

Phosphoenolpyruvate carboxykinase [ATP]

Gene

pckA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA.UniRule annotation3 Publications

Catalytic activityi

ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2.UniRule annotation1 Publication

Cofactori

Mn2+UniRule annotation5 PublicationsNote: Binds 1 Mn2+ ion per subunit.UniRule annotation5 Publications

Enzyme regulationi

Allosterically activated by calcium. It may represent the only case of a monomeric, allosteric enzyme.4 Publications

Kineticsi

  1. KM=3.8 µM for manganese (at 31 degrees Celsius and pH 7.5)2 Publications
  2. KM=0.11 mM for calcium (at 31 degrees Celsius and pH 7.5)2 Publications
  3. KM=0.31 mM for OAA (at 31 degrees Celsius and pH 7.5)2 Publications
  4. KM=0.51 mM for OAA (at pH 7.5)2 Publications
  5. KM=1.4 mM for magnesium (at 31 degrees Celsius and pH 7.5)2 Publications
  6. KM=11 mM for PEP (at pH 7.5)2 Publications

    Pathwayi: gluconeogenesis

    This protein is involved in the pathway gluconeogenesis, which is part of Carbohydrate biosynthesis.UniRule annotation
    View all proteins of this organism that are known to be involved in the pathway gluconeogenesis and in Carbohydrate biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei65SubstrateUniRule annotation1 Publication1
    Metal bindingi149Calcium; via carbonyl oxygenBy similarity1
    Metal bindingi150Calcium; via carbonyl oxygenBy similarity1
    Metal bindingi152Calcium; via carbonyl oxygenBy similarity1
    Binding sitei207SubstrateUniRule annotation1 Publication1
    Metal bindingi213ManganeseUniRule annotation1 Publication1
    Binding sitei213ATPUniRule annotation6 Publications1
    Binding sitei213SubstrateUniRule annotation1 Publication1
    Metal bindingi232Manganese; via tele nitrogenUniRule annotation1 Publication1
    Binding sitei232ATPUniRule annotation6 Publications1
    Metal bindingi269ManganeseUniRule annotation1 Publication1
    Metal bindingi283Calcium; via carbonyl oxygenBy similarity1
    Binding sitei297ATPUniRule annotation6 Publications1
    Binding sitei333ATPUniRule annotation6 Publications1
    Binding sitei333SubstrateUniRule annotation1 Publication1
    Binding sitei455ATPUniRule annotation6 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi248 – 256ATPUniRule annotation6 Publications9
    Nucleotide bindingi449 – 450ATPUniRule annotation6 Publications2

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-HAMAP
    • calcium ion binding Source: EcoCyc
    • magnesium ion binding Source: EcoCyc
    • phosphoenolpyruvate carboxykinase (ATP) activity Source: EcoCyc

    GO - Biological processi

    • gluconeogenesis Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Gluconeogenesis

    Keywords - Ligandi

    ATP-binding, Calcium, Magnesium, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:PEPCARBOXYKIN-MONOMER.
    ECOL316407:JW3366-MONOMER.
    MetaCyc:PEPCARBOXYKIN-MONOMER.
    BRENDAi4.1.1.49. 2026.
    UniPathwayiUPA00138.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoenolpyruvate carboxykinase [ATP]UniRule annotation (EC:4.1.1.49UniRule annotation)
    Short name:
    PCKUniRule annotation
    Short name:
    PEP carboxykinaseUniRule annotation
    Short name:
    PEPCKUniRule annotation
    Gene namesi
    Name:pckAUniRule annotation
    Synonyms:pck
    Ordered Locus Names:b3403, JW3366
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10688. pck.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi65R → Q: Slightly lower catalytic efficiency compared to wild-type and the affinity binding for OAA is 330-fold higher than for wild-type. 1 Publication1
    Mutagenesisi268D → N in PCK51; altered-activity mutant that catalyzes the conversion from oxaloacetate to pyruvate (OAA decarboxylase activity). 1 Publication1
    Mutagenesisi284G → S in PCK53; shows reduced-activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002038181 – 540Phosphoenolpyruvate carboxykinase [ATP]Add BLAST540

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei87N6-acetyllysineUniRule annotation1 Publication1
    Modified residuei523N6-acetyllysineUniRule annotation1 Publication1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    EPDiP22259.
    PaxDbiP22259.
    PRIDEiP22259.

    Expressioni

    Inductioni

    Induced upon entry into stationary phase and by cyclic AMP (cAMP). Repressed by glucose (catabolite repression) and by CsrA.2 Publications

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation9 Publications

    Protein-protein interaction databases

    IntActiP22259. 4 interactors.
    STRINGi511145.b3403.

    Structurei

    Secondary structure

    1540
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni5 – 7Combined sources3
    Helixi9 – 14Combined sources6
    Beta strandi23 – 26Combined sources4
    Helixi29 – 37Combined sources9
    Helixi43 – 45Combined sources3
    Beta strandi47 – 49Combined sources3
    Beta strandi55 – 57Combined sources3
    Helixi67 – 69Combined sources3
    Beta strandi70 – 73Combined sources4
    Turni76 – 81Combined sources6
    Beta strandi87 – 90Combined sources4
    Beta strandi95 – 97Combined sources3
    Helixi99 – 113Combined sources15
    Beta strandi118 – 128Combined sources11
    Turni129 – 131Combined sources3
    Beta strandi133 – 140Combined sources8
    Helixi142 – 151Combined sources10
    Helixi157 – 161Combined sources5
    Beta strandi166 – 172Combined sources7
    Turni178 – 184Combined sources7
    Beta strandi186 – 188Combined sources3
    Beta strandi190 – 194Combined sources5
    Turni195 – 198Combined sources4
    Beta strandi199 – 204Combined sources6
    Helixi209 – 222Combined sources14
    Helixi224 – 226Combined sources3
    Beta strandi229 – 231Combined sources3
    Beta strandi233 – 237Combined sources5
    Beta strandi243 – 247Combined sources5
    Helixi254 – 258Combined sources5
    Beta strandi263 – 269Combined sources7
    Beta strandi271 – 274Combined sources4
    Beta strandi277 – 281Combined sources5
    Beta strandi283 – 288Combined sources6
    Turni294 – 296Combined sources3
    Helixi298 – 302Combined sources5
    Beta strandi309 – 312Combined sources4
    Beta strandi314 – 316Combined sources3
    Turni317 – 319Combined sources3
    Beta strandi320 – 322Combined sources3
    Beta strandi333 – 337Combined sources5
    Helixi338 – 340Combined sources3
    Beta strandi341 – 344Combined sources4
    Beta strandi347 – 352Combined sources6
    Beta strandi354 – 361Combined sources8
    Beta strandi370 – 373Combined sources4
    Helixi376 – 385Combined sources10
    Beta strandi387 – 391Combined sources5
    Helixi394 – 396Combined sources3
    Beta strandi401 – 405Combined sources5
    Helixi407 – 409Combined sources3
    Helixi411 – 413Combined sources3
    Helixi418 – 432Combined sources15
    Beta strandi435 – 440Combined sources6
    Beta strandi447 – 449Combined sources3
    Helixi452 – 463Combined sources12
    Helixi466 – 469Combined sources4
    Beta strandi472 – 475Combined sources4
    Turni476 – 479Combined sources4
    Beta strandi480 – 484Combined sources5
    Helixi491 – 494Combined sources4
    Helixi496 – 499Combined sources4
    Beta strandi500 – 502Combined sources3
    Helixi503 – 521Combined sources19
    Helixi522 – 524Combined sources3
    Helixi528 – 533Combined sources6
    Helixi534 – 536Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1AQ2X-ray1.90A1-540[»]
    1AYLX-ray1.80A1-540[»]
    1K3CX-ray2.00A1-540[»]
    1K3DX-ray2.00A1-540[»]
    1OENX-ray1.90A1-538[»]
    1OS1X-ray1.80A1-540[»]
    2OLQX-ray1.94A1-540[»]
    2OLRX-ray1.60A1-540[»]
    2PXZX-ray2.23X1-540[»]
    2PY7X-ray2.20X1-540[»]
    ProteinModelPortaliP22259.
    SMRiP22259.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP22259.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the phosphoenolpyruvate carboxykinase [ATP] family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105DJ1. Bacteria.
    COG1866. LUCA.
    HOGENOMiHOG000271471.
    InParanoidiP22259.
    KOiK01610.
    OMAiRFIVKEP.
    PhylomeDBiP22259.

    Family and domain databases

    CDDicd00484. PEPCK_ATP. 1 hit.
    Gene3Di3.40.449.10. 1 hit.
    3.90.228.20. 2 hits.
    HAMAPiMF_00453. PEPCK_ATP. 1 hit.
    InterProiIPR001272. PEP_carboxykinase_ATP.
    IPR013035. PEP_carboxykinase_C.
    IPR008210. PEP_carboxykinase_N.
    IPR015994. PEPCK_ATP_CS.
    [Graphical view]
    PfamiPF01293. PEPCK_ATP. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006294. PEP_crbxkin. 1 hit.
    SUPFAMiSSF68923. SSF68923. 1 hit.
    TIGRFAMsiTIGR00224. pckA. 1 hit.
    PROSITEiPS00532. PEPCK_ATP. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P22259-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRVNNGLTPQ ELEAYGISDV HDIVYNPSYD LLYQEELDPS LTGYERGVLT
    60 70 80 90 100
    NLGAVAVDTG IFTGRSPKDK YIVRDDTTRD TFWWADKGKG KNDNKPLSPE
    110 120 130 140 150
    TWQHLKGLVT RQLSGKRLFV VDAFCGANPD TRLSVRFITE VAWQAHFVKN
    160 170 180 190 200
    MFIRPSDEEL AGFKPDFIVM NGAKCTNPQW KEQGLNSENF VAFNLTERMQ
    210 220 230 240 250
    LIGGTWYGGE MKKGMFSMMN YLLPLKGIAS MHCSANVGEK GDVAVFFGLS
    260 270 280 290 300
    GTGKTTLSTD PKRRLIGDDE HGWDDDGVFN FEGGCYAKTI KLSKEAEPEI
    310 320 330 340 350
    YNAIRRDALL ENVTVREDGT IDFDDGSKTE NTRVSYPIYH IDNIVKPVSK
    360 370 380 390 400
    AGHATKVIFL TADAFGVLPP VSRLTADQTQ YHFLSGFTAK LAGTERGITE
    410 420 430 440 450
    PTPTFSACFG AAFLSLHPTQ YAEVLVKRMQ AAGAQAYLVN TGWNGTGKRI
    460 470 480 490 500
    SIKDTRAIID AILNGSLDNA ETFTLPMFNL AIPTELPGVD TKILDPRNTY
    510 520 530 540
    ASPEQWQEKA ETLAKLFIDN FDKYTDTPAG AALVAAGPKL
    Length:540
    Mass (Da):59,643
    Last modified:November 1, 1995 - v2
    Checksum:iA744D90899F6A8A5
    GO

    Sequence cautioni

    The sequence AAA24301 differs from that shown. Reason: Frameshift at position 456. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti67 – 72PKDKYI → QKISIS in AAA24301 (PubMed:1701430).Curated6
    Sequence conflicti192 – 194AFN → R AA sequence (PubMed:1701430).Curated3
    Sequence conflicti197 – 203ERMQLIG → DRAHAADC AA sequence (PubMed:1701430).Curated7
    Sequence conflicti233C → S in AAA24301 (PubMed:1701430).Curated1
    Sequence conflicti252T → N in AAA24301 (PubMed:1701430).Curated1
    Sequence conflicti256 – 260TLSTD → AFPR in AAA24301 (PubMed:1701430).Curated5
    Sequence conflicti281 – 285FEGGC → LKAAG in AAA24301 (PubMed:1701430).Curated5
    Sequence conflicti302 – 307NAIRRD → KLSVVM in AAA24301 (PubMed:1701430).Curated6
    Sequence conflicti346K → R in AAA24301 (PubMed:1701430).Curated1
    Sequence conflicti354 – 359ATKVIF → GRRLSL in AAA24301 (PubMed:1701430).Curated6
    Sequence conflicti363D → H in AAA24301 (PubMed:1701430).Curated1
    Sequence conflicti446T → S in AAA24301 (PubMed:1701430).Curated1
    Sequence conflicti449R → S in AAA24301 (PubMed:1701430).Curated1
    Sequence conflicti460 – 467DAILNGSL → RRHPQRFV (PubMed:6292200).Curated8
    Sequence conflicti499T → R (PubMed:6292200).Curated1

    Mass spectrometryi

    Molecular mass is 59656 Da from positions 1 - 540. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M59823 Genomic DNA. Translation: AAA24301.1. Frameshift.
    U18997 Genomic DNA. Translation: AAA58200.1.
    U00096 Genomic DNA. Translation: AAC76428.1.
    AP009048 Genomic DNA. Translation: BAE77888.1.
    J01656 Unassigned RNA. No translation available.
    S76268 Genomic DNA. Translation: AAB33745.2.
    S76269 Genomic DNA. Translation: AAB33746.2.
    U21325 Genomic DNA. Translation: AAA95999.1.
    PIRiF65135.
    RefSeqiNP_417862.1. NC_000913.3.
    WP_001265681.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76428; AAC76428; b3403.
    BAE77888; BAE77888; BAE77888.
    GeneIDi945667.
    KEGGiecj:JW3366.
    eco:b3403.
    PATRICi32122242. VBIEscCol129921_3498.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M59823 Genomic DNA. Translation: AAA24301.1. Frameshift.
    U18997 Genomic DNA. Translation: AAA58200.1.
    U00096 Genomic DNA. Translation: AAC76428.1.
    AP009048 Genomic DNA. Translation: BAE77888.1.
    J01656 Unassigned RNA. No translation available.
    S76268 Genomic DNA. Translation: AAB33745.2.
    S76269 Genomic DNA. Translation: AAB33746.2.
    U21325 Genomic DNA. Translation: AAA95999.1.
    PIRiF65135.
    RefSeqiNP_417862.1. NC_000913.3.
    WP_001265681.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1AQ2X-ray1.90A1-540[»]
    1AYLX-ray1.80A1-540[»]
    1K3CX-ray2.00A1-540[»]
    1K3DX-ray2.00A1-540[»]
    1OENX-ray1.90A1-538[»]
    1OS1X-ray1.80A1-540[»]
    2OLQX-ray1.94A1-540[»]
    2OLRX-ray1.60A1-540[»]
    2PXZX-ray2.23X1-540[»]
    2PY7X-ray2.20X1-540[»]
    ProteinModelPortaliP22259.
    SMRiP22259.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP22259. 4 interactors.
    STRINGi511145.b3403.

    Proteomic databases

    EPDiP22259.
    PaxDbiP22259.
    PRIDEiP22259.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76428; AAC76428; b3403.
    BAE77888; BAE77888; BAE77888.
    GeneIDi945667.
    KEGGiecj:JW3366.
    eco:b3403.
    PATRICi32122242. VBIEscCol129921_3498.

    Organism-specific databases

    EchoBASEiEB0682.
    EcoGeneiEG10688. pck.

    Phylogenomic databases

    eggNOGiENOG4105DJ1. Bacteria.
    COG1866. LUCA.
    HOGENOMiHOG000271471.
    InParanoidiP22259.
    KOiK01610.
    OMAiRFIVKEP.
    PhylomeDBiP22259.

    Enzyme and pathway databases

    UniPathwayiUPA00138.
    BioCyciEcoCyc:PEPCARBOXYKIN-MONOMER.
    ECOL316407:JW3366-MONOMER.
    MetaCyc:PEPCARBOXYKIN-MONOMER.
    BRENDAi4.1.1.49. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP22259.
    PROiP22259.

    Family and domain databases

    CDDicd00484. PEPCK_ATP. 1 hit.
    Gene3Di3.40.449.10. 1 hit.
    3.90.228.20. 2 hits.
    HAMAPiMF_00453. PEPCK_ATP. 1 hit.
    InterProiIPR001272. PEP_carboxykinase_ATP.
    IPR013035. PEP_carboxykinase_C.
    IPR008210. PEP_carboxykinase_N.
    IPR015994. PEPCK_ATP_CS.
    [Graphical view]
    PfamiPF01293. PEPCK_ATP. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006294. PEP_crbxkin. 1 hit.
    SUPFAMiSSF68923. SSF68923. 1 hit.
    TIGRFAMsiTIGR00224. pckA. 1 hit.
    PROSITEiPS00532. PEPCK_ATP. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPCKA_ECOLI
    AccessioniPrimary (citable) accession number: P22259
    Secondary accession number(s): Q2M768
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1991
    Last sequence update: November 1, 1995
    Last modified: November 2, 2016
    This is version 156 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

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

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    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.