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Protein

Class B acid phosphatase

Gene

aphA

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

Functioni

Dephosphorylates several organic phosphate monoesters including 3'- and 5'-nucleotides, 2'-deoxy-5'-nucleotides, pNPP, phenyl phosphate, glycerol 2-phosphate, ribose 5-phosphate, O-phospho-L-amino acids and phytic acid, showing the highest activity with aryl phosphoesters (pNPP, phenyl phosphate and O-phospho-L-tyrosine), and to a lesser extent with 3'- and 5'-nucleotides. No activity toward ATP, phosphodiesters, glycerol-1-phosphate, glucose 1-phosphate, glucose 6-phosphate, NADP, GTP or 3',5'-cAMP, ADP or ATP. Also has a phosphotransferase activity catalyzing the transfer of low-energy phosphate groups from organic phosphate monoesters to free hydroxyl groups of various organic compounds. Capable of transferring phosphate from either pNPP or UMP to adenosine or uridine. Does not exhibit nucleotide phosphomutase activity.2 Publications

Catalytic activityi

A phosphate monoester + H2O = an alcohol + phosphate.4 Publications

Cofactori

Mg2+3 PublicationsNote: Binds 1 Mg2+ ion per subunit.3 Publications

Enzyme regulationi

Activated by ethanol. Inhibited strongly by EDTA and more weakly by other divalent ions chelators 1,10-phenanthroline, EGTA and dipicolinic acid. Inhibited also by nucleosides, inorganic phosphate and Ca2+. Unaffected by F-.2 Publications

Kineticsi

  1. KM=3.0 µM for 5'-AMP (at 37 degrees Celsius)2 Publications
  2. KM=15.0 µM for 5'-GMP (at 37 degrees Celsius)2 Publications
  3. KM=15.0 µM for 5'-UMP (at 37 degrees Celsius)2 Publications
  4. KM=138.0 µM for 5'-CMP (at 37 degrees Celsius)2 Publications
  5. KM=0.9 µM for 3'-AMP (at 37 degrees Celsius)2 Publications
  6. KM=1.7 µM for 3'-GMP (at 37 degrees Celsius)2 Publications
  7. KM=1.2 µM for 3'-UMP (at 37 degrees Celsius)2 Publications
  8. KM=9.0 µM for 3'-CMP (at 37 degrees Celsius)2 Publications
  9. KM=0.8 µM for 5'-dAMP (at 37 degrees Celsius)2 Publications
  10. KM=3.0 µM for 5'-dGMP (at 37 degrees Celsius)2 Publications
  11. KM=10.0 µM for 5'-dUMP (at 37 degrees Celsius)2 Publications
  12. KM=35.0 µM for 5'-dCMP (at 37 degrees Celsius)2 Publications
  13. KM=1.5 µM for 3'-dAMP (at 37 degrees Celsius)2 Publications
  14. KM=1.6 µM for 3'-dGMP (at 37 degrees Celsius)2 Publications
  15. KM=0.9 µM for 3'-dUMP (at 37 degrees Celsius)2 Publications
  16. KM=1.3 µM for 3'-dCMP (at 37 degrees Celsius)2 Publications
  17. KM=169.0 µM for pNPP (at 37 degrees Celsius)2 Publications
  18. KM=980.0 µM for ribose 5-phosphate (at 37 degrees Celsius)2 Publications
  19. KM=1288.0 µM for glucose 6-phosphate (at 37 degrees Celsius)2 Publications
  20. KM=666.0 µM for beta-glycerol phosphate (at 37 degrees Celsius)2 Publications

    pH dependencei

    Optimum pH is 6-6.5 with 5'-AMP as substrate, and pH 5.5-6 with 3'-AMP or pNPP as substrate.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei69 – 691Nucleophile
    Metal bindingi69 – 691Magnesium
    Active sitei71 – 711Proton donor
    Metal bindingi71 – 711Magnesium; via carbonyl oxygen
    Binding sitei177 – 1771Substrate
    Metal bindingi192 – 1921Magnesium

    GO - Molecular functioni

    • acid phosphatase activity Source: EcoCyc
    • cofactor binding Source: EcoCyc
    • metal ion binding Source: UniProtKB-KW
    • phosphoserine phosphatase activity Source: EcoCyc

    GO - Biological processi

    • dephosphorylation Source: GOC
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:APHA-MONOMER.
    ECOL316407:JW4015-MONOMER.
    MetaCyc:APHA-MONOMER.
    BRENDAi3.1.3.2. 2026.
    SABIO-RKP0AE22.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Class B acid phosphatase (EC:3.1.3.2)
    Short name:
    CBAP
    Gene namesi
    Name:aphA
    Synonyms:napA, yjbP
    Ordered Locus Names:b4055, JW4015
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11934. aphA.

    Subcellular locationi

    • Periplasm 1 Publication

    GO - Cellular componenti

    • outer membrane-bounded periplasmic space Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Periplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2525Or 231 PublicationAdd
    BLAST
    Chaini26 – 237212Class B acid phosphatasePRO_0000024004Add
    BLAST

    Proteomic databases

    PaxDbiP0AE22.
    PRIDEiP0AE22.

    Interactioni

    Subunit structurei

    Homotetramer.4 Publications

    Protein-protein interaction databases

    DIPiDIP-9116N.
    IntActiP0AE22. 2 interactions.
    MINTiMINT-1294190.
    STRINGi511145.b4055.

    Structurei

    Secondary structure

    1
    237
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi37 – 415Combined sources
    Beta strandi47 – 493Combined sources
    Helixi51 – 577Combined sources
    Turni58 – 603Combined sources
    Beta strandi65 – 684Combined sources
    Turni72 – 743Combined sources
    Helixi78 – 8811Combined sources
    Helixi94 – 974Combined sources
    Helixi99 – 1068Combined sources
    Helixi109 – 1124Combined sources
    Beta strandi113 – 1153Combined sources
    Helixi117 – 12913Combined sources
    Beta strandi132 – 1376Combined sources
    Helixi147 – 1548Combined sources
    Turni159 – 1613Combined sources
    Beta strandi169 – 1713Combined sources
    Helixi178 – 1836Combined sources
    Beta strandi186 – 1938Combined sources
    Helixi194 – 2029Combined sources
    Beta strandi206 – 2094Combined sources
    Turni224 – 2274Combined sources
    Beta strandi230 – 2323Combined sources
    Turni233 – 2364Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1N8NX-ray1.69A26-237[»]
    1N9KX-ray2.20A/B26-237[»]
    1RMQX-ray2.00A/B26-237[»]
    1RMTX-ray1.40A/B/C/D26-237[»]
    1RMYX-ray1.75A/B26-237[»]
    2B82X-ray1.25A/B27-237[»]
    2B8JX-ray2.03A/B27-237[»]
    2G1AX-ray2.00A/B26-237[»]
    2HEGX-ray1.50A/B27-237[»]
    2HF7X-ray1.60A/B27-237[»]
    3CZ4X-ray1.70A26-237[»]
    ProteinModelPortaliP0AE22.
    SMRiP0AE22. Positions 27-237.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AE22.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni137 – 1382Substrate binding

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG3700.
    HOGENOMiHOG000270623.
    KOiK03788.
    OMAiYFITGRT.
    OrthoDBiEOG6HTNVZ.

    Family and domain databases

    Gene3Di3.40.50.1000. 1 hit.
    InterProiIPR005519. Acid_phosphat_B.
    IPR023214. HAD-like_dom.
    IPR010025. HAD-SF_ppase_IIIB_AphA.
    [Graphical view]
    PfamiPF03767. Acid_phosphat_B. 1 hit.
    [Graphical view]
    PIRSFiPIRSF017818. Acid_Ptase_B. 1 hit.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01672. AphA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P0AE22-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRKITQAISA VCLLFALNSS AVALASSPSP LNPGTNVARL AEQAPIHWVS
    60 70 80 90 100
    VAQIENSLAG RPPMAVGFDI DDTVLFSSPG FWRGKKTFSP ESEDYLKNPV
    110 120 130 140 150
    FWEKMNNGWD EFSIPKEVAR QLIDMHVRRG DAIFFVTGRS PTKTETVSKT
    160 170 180 190 200
    LADNFHIPAT NMNPVIFAGD KPGQNTKSQW LQDKNIRIFY GDSDNDITAA
    210 220 230
    RDVGARGIRI LRASNSTYKP LPQAGAFGEE VIVNSEY
    Length:237
    Mass (Da):26,104
    Last modified:December 6, 2005 - v1
    Checksum:i35C1BFE6DF9E530D
    GO

    Sequence cautioni

    The sequence AAC43149.1 differs from that shown. Reason: Frameshift at position 62. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U51210 Genomic DNA. Translation: AAA96322.1.
    X86971 Genomic DNA. Translation: CAA60534.1.
    U00006 Genomic DNA. Translation: AAC43149.1. Frameshift.
    U00096 Genomic DNA. Translation: AAC77025.1.
    AP009048 Genomic DNA. Translation: BAE78057.1.
    PIRiS54790.
    RefSeqiNP_418479.1. NC_000913.3.
    WP_001226928.1. NZ_CP010445.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77025; AAC77025; b4055.
    BAE78057; BAE78057; BAE78057.
    GeneIDi948562.
    KEGGieco:b4055.
    PATRICi32123655. VBIEscCol129921_4176.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U51210 Genomic DNA. Translation: AAA96322.1.
    X86971 Genomic DNA. Translation: CAA60534.1.
    U00006 Genomic DNA. Translation: AAC43149.1. Frameshift.
    U00096 Genomic DNA. Translation: AAC77025.1.
    AP009048 Genomic DNA. Translation: BAE78057.1.
    PIRiS54790.
    RefSeqiNP_418479.1. NC_000913.3.
    WP_001226928.1. NZ_CP010445.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1N8NX-ray1.69A26-237[»]
    1N9KX-ray2.20A/B26-237[»]
    1RMQX-ray2.00A/B26-237[»]
    1RMTX-ray1.40A/B/C/D26-237[»]
    1RMYX-ray1.75A/B26-237[»]
    2B82X-ray1.25A/B27-237[»]
    2B8JX-ray2.03A/B27-237[»]
    2G1AX-ray2.00A/B26-237[»]
    2HEGX-ray1.50A/B27-237[»]
    2HF7X-ray1.60A/B27-237[»]
    3CZ4X-ray1.70A26-237[»]
    ProteinModelPortaliP0AE22.
    SMRiP0AE22. Positions 27-237.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-9116N.
    IntActiP0AE22. 2 interactions.
    MINTiMINT-1294190.
    STRINGi511145.b4055.

    Proteomic databases

    PaxDbiP0AE22.
    PRIDEiP0AE22.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77025; AAC77025; b4055.
    BAE78057; BAE78057; BAE78057.
    GeneIDi948562.
    KEGGieco:b4055.
    PATRICi32123655. VBIEscCol129921_4176.

    Organism-specific databases

    EchoBASEiEB1878.
    EcoGeneiEG11934. aphA.

    Phylogenomic databases

    eggNOGiCOG3700.
    HOGENOMiHOG000270623.
    KOiK03788.
    OMAiYFITGRT.
    OrthoDBiEOG6HTNVZ.

    Enzyme and pathway databases

    BioCyciEcoCyc:APHA-MONOMER.
    ECOL316407:JW4015-MONOMER.
    MetaCyc:APHA-MONOMER.
    BRENDAi3.1.3.2. 2026.
    SABIO-RKP0AE22.

    Miscellaneous databases

    EvolutionaryTraceiP0AE22.
    PROiP0AE22.

    Family and domain databases

    Gene3Di3.40.50.1000. 1 hit.
    InterProiIPR005519. Acid_phosphat_B.
    IPR023214. HAD-like_dom.
    IPR010025. HAD-SF_ppase_IIIB_AphA.
    [Graphical view]
    PfamiPF03767. Acid_phosphat_B. 1 hit.
    [Graphical view]
    PIRSFiPIRSF017818. Acid_Ptase_B. 1 hit.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01672. AphA. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Marquez S.M., Gumport R.I.
      Submitted (MAR-1996) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. "Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product."
      Thaller M.C., Schippa S., Bonci A., Cresti S., Rossolini G.M.
      FEMS Microbiol. Lett. 146:191-198(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBSTRATE SPECIFICITY, SUBCELLULAR LOCATION, SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes."
      Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.
      Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION.
      Strain: K12 / MG1655 / ATCC 47076.
    5. "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.
    6. "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 26-37.
      Strain: K12 / EMG2.
    7. "Expression, purification, crystallization and preliminary X-ray characterization of the class B acid phosphatase (AphA) from Escherichia coli."
      Forleo C., Benvenuti M., Calderone V., Schippa S., Docquier J.D., Thaller M.C., Rossolini G.M., Mangani S.
      Acta Crystallogr. D 59:1058-1060(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION, CATALYTIC ACTIVITY, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: K12 / MG1655 / ATCC 47076.
    8. "Biochemical characterization of the class B acid phosphatase (AphA) of Escherichia coli MG1655."
      Passariello C., Forleo C., Micheli V., Schippa S., Leone R., Mangani S., Thaller M.C., Rossolini G.M.
      Biochim. Biophys. Acta 1764:13-19(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY.
      Strain: K12 / MG1655 / ATCC 47076.
    9. "The first structure of a bacterial class B acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold."
      Calderone V., Forleo C., Benvenuti M., Cristina Thaller M., Maria Rossolini G., Mangani S.
      J. Mol. Biol. 335:761-773(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 26-237 IN COMPLEXES WITH MAGNESIUM IONS, COFACTOR, SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.
    10. "A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases."
      Calderone V., Forleo C., Benvenuti M., Thaller M.C., Rossolini G.M., Mangani S.
      J. Mol. Biol. 355:708-721(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 26-237 IN COMPLEXES WITH REACTION INTERMEDIATE ANALOG; REACTION PRODUCTS; PHOSPHATE AND MAGNESIUM IONS, COFACTOR, REACTION MECHANISM, SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.
    11. "Structural insights into the catalytic mechanism of the bacterial class B phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases."
      Leone R., Cappelletti E., Benvenuti M., Lentini G., Thaller M.C., Mangani S.
      J. Mol. Biol. 384:478-488(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 26-237 IN COMPLEXES WITH SUBSTRATE ANALOG INHIBITOR; TRANSITION STATE ANALOG; REACTION INTERMEDIATE ANALOG AND MAGNESIUM IONS, CATALYTIC ACTIVITY, COFACTOR, REACTION MECHANISM, SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiAPHA_ECOLI
    AccessioniPrimary (citable) accession number: P0AE22
    Secondary accession number(s): P32697
    , P76787, Q2M6P9, Q57085
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 6, 2005
    Last sequence update: December 6, 2005
    Last modified: July 22, 2015
    This is version 93 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

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

    Documents

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