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P22259 (PCKA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 139. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Phosphoenolpyruvate carboxykinase [ATP]

Short name=PCK
Short name=PEP carboxykinase
Short name=PEPCK
EC=4.1.1.49
Gene names
Name:pckA
Synonyms:pck
Ordered Locus Names:b3403, JW3366
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length540 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA. Ref.1 Ref.8 Ref.10

Catalytic activity

ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2. Ref.8

Cofactor

Binds 1 manganese ion per subunit. Ref.1 Ref.16 Ref.19 Ref.20 Ref.21

Enzyme regulation

Allosterically activated by calcium. It may represent the only case of a monomeric, allosteric enzyme. Ref.1 Ref.8 Ref.14 Ref.18

Pathway

Carbohydrate biosynthesis; gluconeogenesis. HAMAP-Rule MF_00453

Subunit structure

Monomer. Ref.1 Ref.8 Ref.16 Ref.18

Subcellular location

Cytoplasm HAMAP-Rule MF_00453.

Induction

Induced upon entry into stationary phase and by cyclic AMP (cAMP). Repressed by glucose (catabolite repression) and by CsrA. Ref.1 Ref.8 Ref.9 Ref.11 Ref.14 Ref.18

Sequence similarities

Belongs to the phosphoenolpyruvate carboxykinase [ATP] family.

Biophysicochemical properties

Kinetic parameters:

KM=3.8 µM for manganese (at 31 degrees Celsius and pH 7.5) Ref.8 Ref.19

KM=0.11 mM for calcium (at 31 degrees Celsius and pH 7.5)

KM=0.31 mM for OAA (at 31 degrees Celsius and pH 7.5)

KM=0.51 mM for OAA (at pH 7.5)

KM=1.4 mM for magnesium (at 31 degrees Celsius and pH 7.5)

KM=11 mM for PEP (at pH 7.5)

Mass spectrometry

Molecular mass is 59656 Da from positions 1 - 540. Determined by ESI. Ref.14

Sequence caution

The sequence AAA24301.1 differs from that shown. Reason: Frameshift at position 456. Translation N-terminally extended.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 540540Phosphoenolpyruvate carboxykinase [ATP] HAMAP-Rule MF_00453
PRO_0000203818

Regions

Nucleotide binding248 – 2569ATP HAMAP-Rule MF_00453
Nucleotide binding449 – 4502ATP HAMAP-Rule MF_00453

Sites

Metal binding1491Calcium; via carbonyl oxygen By similarity
Metal binding1501Calcium; via carbonyl oxygen By similarity
Metal binding1521Calcium; via carbonyl oxygen By similarity
Metal binding2131Manganese
Metal binding2321Manganese; via tele nitrogen
Metal binding2691Manganese
Metal binding2831Calcium; via carbonyl oxygen By similarity
Binding site651Substrate
Binding site2071Substrate
Binding site2131ATP
Binding site2131Substrate
Binding site2321ATP
Binding site2971ATP
Binding site3331ATP
Binding site3331Substrate
Binding site4551ATP

Amino acid modifications

Modified residue871N6-acetyllysine Ref.13
Modified residue5231N6-acetyllysine Ref.13

Experimental info

Mutagenesis651R → Q: Slightly lower catalytic efficiency compared to wild-type and the affinity binding for OAA is 330-fold higher than for wild-type. Ref.19
Mutagenesis2681D → N in PCK51; altered-activity mutant that catalyzes the conversion from oxaloacetate to pyruvate (OAA decarboxylase activity). Ref.6
Mutagenesis2841G → S in PCK53; shows reduced-activity. Ref.6
Sequence conflict67 – 726PKDKYI → QKISIS in AAA24301. Ref.1
Sequence conflict192 – 1943AFN → R AA sequence Ref.1
Sequence conflict197 – 2037ERMQLIG → DRAHAADC AA sequence Ref.1
Sequence conflict2331C → S in AAA24301. Ref.1
Sequence conflict2521T → N in AAA24301. Ref.1
Sequence conflict256 – 2605TLSTD → AFPR in AAA24301. Ref.1
Sequence conflict281 – 2855FEGGC → LKAAG in AAA24301. Ref.1
Sequence conflict302 – 3076NAIRRD → KLSVVM in AAA24301. Ref.1
Sequence conflict3461K → R in AAA24301. Ref.1
Sequence conflict354 – 3596ATKVIF → GRRLSL in AAA24301. Ref.1
Sequence conflict3631D → H in AAA24301. Ref.1
Sequence conflict4461T → S in AAA24301. Ref.1
Sequence conflict4491R → S in AAA24301. Ref.1
Sequence conflict460 – 4678DAILNGSL → RRHPQRFV Ref.4
Sequence conflict4991T → R Ref.4

Secondary structure

......................................................................................................................... 540
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P22259 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: A744D90899F6A8A5

FASTA54059,643
        10         20         30         40         50         60 
MRVNNGLTPQ ELEAYGISDV HDIVYNPSYD LLYQEELDPS LTGYERGVLT NLGAVAVDTG 

        70         80         90        100        110        120 
IFTGRSPKDK YIVRDDTTRD TFWWADKGKG KNDNKPLSPE TWQHLKGLVT RQLSGKRLFV 

       130        140        150        160        170        180 
VDAFCGANPD TRLSVRFITE VAWQAHFVKN MFIRPSDEEL AGFKPDFIVM NGAKCTNPQW 

       190        200        210        220        230        240 
KEQGLNSENF VAFNLTERMQ LIGGTWYGGE MKKGMFSMMN YLLPLKGIAS MHCSANVGEK 

       250        260        270        280        290        300 
GDVAVFFGLS GTGKTTLSTD PKRRLIGDDE HGWDDDGVFN FEGGCYAKTI KLSKEAEPEI 

       310        320        330        340        350        360 
YNAIRRDALL ENVTVREDGT IDFDDGSKTE NTRVSYPIYH IDNIVKPVSK AGHATKVIFL 

       370        380        390        400        410        420 
TADAFGVLPP VSRLTADQTQ YHFLSGFTAK LAGTERGITE PTPTFSACFG AAFLSLHPTQ 

       430        440        450        460        470        480 
YAEVLVKRMQ AAGAQAYLVN TGWNGTGKRI SIKDTRAIID AILNGSLDNA ETFTLPMFNL 

       490        500        510        520        530        540 
AIPTELPGVD TKILDPRNTY ASPEQWQEKA ETLAKLFIDN FDKYTDTPAG AALVAAGPKL 

« Hide

References

« Hide 'large scale' references
[1]"Sequence of the pckA gene of Escherichia coli K-12: relevance to genetic and allosteric regulation and homology of E. coli phosphoenolpyruvate carboxykinase with the enzymes from Trypanosoma brucei and Saccharomyces cerevisiae."
Medina V., Pontarollo R., Glaeske D., Tabel H., Goldie H.
J. Bacteriol. 172:7151-7156(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, FUNCTION, ENZYME REGULATION, COFACTOR, SUBUNIT.
Strain: K12.
[2]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"Osmoregulation of gene expression. II. DNA sequence of the envZ gene of the ompB operon of Escherichia coli and characterization of its gene product."
Mizuno T., Wurtzel E.T., Inouye M.
J. Biol. Chem. 257:13692-13698(1982) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 439-540.
[5]"The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli."
Ramseier T.M., Bledig S., Michotey V., Feghali R., Saier M.H. Jr.
Mol. Microbiol. 16:1157-1169(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-39.
Strain: K12.
[6]"A mutant phosphoenolpyruvate carboxykinase in Escherichia coli conferring oxaloacetate decarboxylase activity."
Hou S.-Y., Chao Y.-P., Liao J.C.
J. Bacteriol. 177:1620-1623(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 242-290, MUTAGENESIS OF ASP-268 AND GLY-284.
[7]"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
Link A.J., Robison K., Church G.M.
Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-12.
Strain: K12 / EMG2.
[8]"Allosteric control by calcium and mechanism of desensitization of phosphoenolpyruvate carboxykinase of Escherichia coli."
Goldie A.H., Sanwal B.D.
J. Biol. Chem. 255:1399-1405(1980) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
[9]"Regulation of transcription of the Escherichia coli phosphoenolpyruvate carboxykinase locus: studies with pck-lacZ operon fusions."
Goldie H.
J. Bacteriol. 159:832-836(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION.
[10]"Control of gluconeogenic growth by pps and pck in Escherichia coli."
Chao Y.P., Patnaik R., Roof W.D., Young R.F., Liao J.C.
J. Bacteriol. 175:6939-6944(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN GLUCONEOGENESIS.
[11]"Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties."
Romeo T., Gong M., Liu M.-Y., Brun-Zinkernagel A.-M.
J. Bacteriol. 175:4744-4755(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION.
[12]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[13]"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-87 AND LYS-523, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[14]"Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase: a new structural family with the P-loop nucleoside triphosphate hydrolase fold."
Matte A., Goldie H., Sweet R.M., Delbaere L.T.J.
J. Mol. Biol. 256:126-143(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-538, ENZYME REGULATION, MASS SPECTROMETRY.
[15]"Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase."
Tari L.W., Matte A., Pugazhenthi U., Goldie H., Delbaere L.T.J.
Nat. Struct. Biol. 3:355-363(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH ATP AND SUBSTRATE ANALOGS, REACTION MECHANISM.
[16]"Mg(2+)-Mn(2+) clusters in enzyme-catalyzed phosphoryl-transfer reactions."
Tari L.W., Matte A., Goldie H., Delbaere L.T.
Nat. Struct. Biol. 4:990-994(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH ATP, MANGANESE AND SUBSTRATE, COFACTOR, SUBUNIT.
[17]"The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3)."
Sudom A.M., Prasad L., Goldie H., Delbaere L.T.
J. Mol. Biol. 314:83-92(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH ATP ANALOGS AND SUBSTRATE, REACTION MECHANISM.
[18]"Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin."
Sudom A., Walters R., Pastushok L., Goldie D., Prasad L., Delbaere L.T., Goldie H.
J. Bacteriol. 185:4233-4242(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH ATP, CALCIUM AND SUBSTRATE, ENZYME REGULATION, REACTION MECHANISM, SUBUNIT.
[19]"How does an enzyme recognize CO2?"
Cotelesage J.J., Puttick J., Goldie H., Rajabi B., Novakovski B., Delbaere L.T.
Int. J. Biochem. Cell Biol. 39:1204-1210(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH ATP, MANGANESE AND SUBSTRATE ANALOGS, MUTAGENESIS OF ARG-65, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
[20]"Crystal structure of E. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ATP, Mg2+, Mn2+, carbon dioxide and oxaloacetate."
Delbaere L.T.J., Cotelesage J.J.H., Goldie H.
Submitted (MAY-2007) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.23 ANGSTROMS) IN COMPLEX WITH ATP, MANGANESE AND SUBSTRATE ANALOGS, COFACTOR.
[21]"Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser."
Delbaere L.T.J., Cotelesage J.J.H., Goldie H.
Submitted (MAY-2007) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH ATP AND MANGANESE, COFACTOR.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRF65135.
RefSeqNP_417862.1. NC_000913.3.
YP_492029.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP22259.
SMRP22259. Positions 6-540.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP22259. 4 interactions.
STRING511145.b3403.

PTM databases

PhosSiteP0809417.

Proteomic databases

PaxDbP22259.
PRIDEP22259.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76428; AAC76428; b3403.
BAE77888; BAE77888; BAE77888.
GeneID12933187.
945667.
KEGGecj:Y75_p3773.
eco:b3403.
PATRIC32122242. VBIEscCol129921_3498.

Organism-specific databases

EchoBASEEB0682.
EcoGeneEG10688. pck.

Phylogenomic databases

eggNOGCOG1866.
HOGENOMHOG000271471.
KOK01610.
OMARYAGEMK.
OrthoDBEOG6DG2RK.
PhylomeDBP22259.
ProtClustDBPRK09344.

Enzyme and pathway databases

BioCycEcoCyc:PEPCARBOXYKIN-MONOMER.
ECOL316407:JW3366-MONOMER.
MetaCyc:PEPCARBOXYKIN-MONOMER.
UniPathwayUPA00138.

Gene expression databases

GenevestigatorP22259.

Family and domain databases

Gene3D3.40.449.10. 1 hit.
3.90.228.20. 2 hits.
HAMAPMF_00453. PEPCK_ATP.
InterProIPR001272. PEP_carboxykinase_ATP.
IPR013035. PEP_carboxykinase_C.
IPR008210. PEP_carboxykinase_N.
IPR015994. PEPCK_ATP_CS.
[Graphical view]
PfamPF01293. PEPCK_ATP. 1 hit.
[Graphical view]
PIRSFPIRSF006294. PEP_crbxkin. 1 hit.
SUPFAMSSF68923. SSF68923. 1 hit.
TIGRFAMsTIGR00224. pckA. 1 hit.
PROSITEPS00532. PEPCK_ATP. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP22259.
PROP22259.

Entry information

Entry namePCKA_ECOLI
AccessionPrimary (citable) accession number: P22259
Secondary accession number(s): Q2M768
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: November 1, 1995
Last modified: April 16, 2014
This is version 139 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene