APHA_ECOLI
ID APHA_ECOLI Reviewed; 237 AA.
AC P0AE22; P32697; P76787; Q2M6P9; Q57085;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Class B acid phosphatase;
DE Short=CBAP;
DE EC=3.1.3.2;
DE Flags: Precursor;
GN Name=aphA; Synonyms=napA, yjbP; OrderedLocusNames=b4055, JW4015;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Marquez S.M., Gumport R.I.;
RL Submitted (MAR-1996) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, SUBSTRATE SPECIFICITY,
RP SUBCELLULAR LOCATION, AND SUBUNIT.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9011040; DOI=10.1111/j.1574-6968.1997.tb10192.x;
RA Thaller M.C., Schippa S., Bonci A., Cresti S., Rossolini G.M.;
RT "Identification of the gene (aphA) encoding the class B acid
RT phosphatase/phosphotransferase of Escherichia coli MG1655 and
RT characterization of its product.";
RL FEMS Microbiol. Lett. 146:191-198(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP PROTEIN SEQUENCE OF 26-37.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [7]
RP CRYSTALLIZATION, CATALYTIC ACTIVITY, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=12777773; DOI=10.1107/s0907444903006826;
RA Forleo C., Benvenuti M., Calderone V., Schippa S., Docquier J.D.,
RA Thaller M.C., Rossolini G.M., Mangani S.;
RT "Expression, purification, crystallization and preliminary X-ray
RT characterization of the class B acid phosphatase (AphA) from Escherichia
RT coli.";
RL Acta Crystallogr. D 59:1058-1060(2003).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBSTRATE SPECIFICITY.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16297670; DOI=10.1016/j.bbapap.2005.08.028;
RA Passariello C., Forleo C., Micheli V., Schippa S., Leone R., Mangani S.,
RA Thaller M.C., Rossolini G.M.;
RT "Biochemical characterization of the class B acid phosphatase (AphA) of
RT Escherichia coli MG1655.";
RL Biochim. Biophys. Acta 1764:13-19(2006).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 26-237 IN COMPLEXES WITH
RP MAGNESIUM IONS, COFACTOR, AND SUBUNIT.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=14687572; DOI=10.1016/j.jmb.2003.10.050;
RA Calderone V., Forleo C., Benvenuti M., Cristina Thaller M.,
RA Maria Rossolini G., Mangani S.;
RT "The first structure of a bacterial class B acid phosphatase reveals
RT further structural heterogeneity among phosphatases of the haloacid
RT dehalogenase fold.";
RL J. Mol. Biol. 335:761-773(2004).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 26-237 IN COMPLEXES WITH REACTION
RP INTERMEDIATE ANALOG; REACTION PRODUCTS; PHOSPHATE AND MAGNESIUM IONS,
RP COFACTOR, REACTION MECHANISM, AND SUBUNIT.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16330049; DOI=10.1016/j.jmb.2005.10.068;
RA Calderone V., Forleo C., Benvenuti M., Thaller M.C., Rossolini G.M.,
RA Mangani S.;
RT "A structure-based proposal for the catalytic mechanism of the bacterial
RT acid phosphatase AphA belonging to the DDDD superfamily of
RT phosphohydrolases.";
RL J. Mol. Biol. 355:708-721(2006).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 26-237 IN COMPLEXES WITH SUBSTRATE
RP ANALOG INHIBITOR; TRANSITION STATE ANALOG; REACTION INTERMEDIATE ANALOG AND
RP MAGNESIUM IONS, CATALYTIC ACTIVITY, COFACTOR, REACTION MECHANISM, AND
RP SUBUNIT.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=18845157; DOI=10.1016/j.jmb.2008.09.050;
RA Leone R., Cappelletti E., Benvenuti M., Lentini G., Thaller M.C.,
RA Mangani S.;
RT "Structural insights into the catalytic mechanism of the bacterial class B
RT phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases.";
RL J. Mol. Biol. 384:478-488(2008).
CC -!- FUNCTION: Dephosphorylates several organic phosphate monoesters
CC including 3'- and 5'-nucleotides, 2'-deoxy-5'-nucleotides, pNPP, phenyl
CC phosphate, glycerol 2-phosphate, ribose 5-phosphate, O-phospho-L-amino
CC acids and phytic acid, showing the highest activity with aryl
CC phosphoesters (pNPP, phenyl phosphate and O-phospho-L-tyrosine), and to
CC a lesser extent with 3'- and 5'-nucleotides. No activity toward ATP,
CC phosphodiesters, glycerol-1-phosphate, glucose 1-phosphate, glucose 6-
CC phosphate, NADP, GTP or 3',5'-cAMP, ADP or ATP. Also has a
CC phosphotransferase activity catalyzing the transfer of low-energy
CC phosphate groups from organic phosphate monoesters to free hydroxyl
CC groups of various organic compounds. Capable of transferring phosphate
CC from either pNPP or UMP to adenosine or uridine. Does not exhibit
CC nucleotide phosphomutase activity. {ECO:0000269|PubMed:16297670,
CC ECO:0000269|PubMed:9011040}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a phosphate monoester + H2O = an alcohol + phosphate;
CC Xref=Rhea:RHEA:15017, ChEBI:CHEBI:15377, ChEBI:CHEBI:30879,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:67140; EC=3.1.3.2;
CC Evidence={ECO:0000269|PubMed:12777773, ECO:0000269|PubMed:16297670,
CC ECO:0000269|PubMed:18845157, ECO:0000269|PubMed:9011040};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:14687572, ECO:0000269|PubMed:16330049,
CC ECO:0000269|PubMed:18845157};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:14687572,
CC ECO:0000269|PubMed:16330049, ECO:0000269|PubMed:18845157};
CC -!- ACTIVITY REGULATION: Activated by ethanol. Inhibited strongly by EDTA
CC and more weakly by other divalent ions chelators 1,10-phenanthroline,
CC EGTA and dipicolinic acid. Inhibited also by nucleosides, inorganic
CC phosphate and Ca(2+). Unaffected by F(-). {ECO:0000269|PubMed:16297670,
CC ECO:0000269|PubMed:9011040}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.0 uM for 5'-AMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=15.0 uM for 5'-GMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=15.0 uM for 5'-UMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=138.0 uM for 5'-CMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=0.9 uM for 3'-AMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=1.7 uM for 3'-GMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=1.2 uM for 3'-UMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=9.0 uM for 3'-CMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=0.8 uM for 5'-dAMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=3.0 uM for 5'-dGMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=10.0 uM for 5'-dUMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=35.0 uM for 5'-dCMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=1.5 uM for 3'-dAMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=1.6 uM for 3'-dGMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=0.9 uM for 3'-dUMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=1.3 uM for 3'-dCMP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=169.0 uM for pNPP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=980.0 uM for ribose 5-phosphate (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=1288.0 uM for glucose 6-phosphate (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC KM=666.0 uM for beta-glycerol phosphate (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:16297670, ECO:0000269|PubMed:9011040};
CC pH dependence:
CC Optimum pH is 6-6.5 with 5'-AMP as substrate, and pH 5.5-6 with 3'-
CC AMP or pNPP as substrate. {ECO:0000269|PubMed:16297670,
CC ECO:0000269|PubMed:9011040};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:14687572,
CC ECO:0000269|PubMed:16330049, ECO:0000269|PubMed:18845157,
CC ECO:0000269|PubMed:9011040}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:9011040}.
CC -!- SIMILARITY: Belongs to the class B bacterial acid phosphatase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC43149.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U51210; AAA96322.1; -; Genomic_DNA.
DR EMBL; X86971; CAA60534.1; -; Genomic_DNA.
DR EMBL; U00006; AAC43149.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U00096; AAC77025.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78057.1; -; Genomic_DNA.
DR PIR; S54790; S54790.
DR RefSeq; NP_418479.1; NC_000913.3.
DR RefSeq; WP_001226928.1; NZ_SSZK01000016.1.
DR PDB; 1N8N; X-ray; 1.69 A; A=26-237.
DR PDB; 1N9K; X-ray; 2.20 A; A/B=26-237.
DR PDB; 1RMQ; X-ray; 2.00 A; A/B=26-237.
DR PDB; 1RMT; X-ray; 1.40 A; A/B/C/D=26-237.
DR PDB; 1RMY; X-ray; 1.75 A; A/B=26-237.
DR PDB; 2B82; X-ray; 1.25 A; A/B=27-237.
DR PDB; 2B8J; X-ray; 2.03 A; A/B=27-237.
DR PDB; 2G1A; X-ray; 2.00 A; A/B=26-237.
DR PDB; 2HEG; X-ray; 1.50 A; A/B=27-237.
DR PDB; 2HF7; X-ray; 1.60 A; A/B=27-237.
DR PDB; 3CZ4; X-ray; 1.70 A; A=26-237.
DR PDBsum; 1N8N; -.
DR PDBsum; 1N9K; -.
DR PDBsum; 1RMQ; -.
DR PDBsum; 1RMT; -.
DR PDBsum; 1RMY; -.
DR PDBsum; 2B82; -.
DR PDBsum; 2B8J; -.
DR PDBsum; 2G1A; -.
DR PDBsum; 2HEG; -.
DR PDBsum; 2HF7; -.
DR PDBsum; 3CZ4; -.
DR AlphaFoldDB; P0AE22; -.
DR SMR; P0AE22; -.
DR BioGRID; 4259337; 14.
DR DIP; DIP-9116N; -.
DR IntAct; P0AE22; 3.
DR STRING; 511145.b4055; -.
DR DrugBank; DB02594; 2'-Deoxycytidine.
DR jPOST; P0AE22; -.
DR PaxDb; P0AE22; -.
DR PRIDE; P0AE22; -.
DR DNASU; 948562; -.
DR EnsemblBacteria; AAC77025; AAC77025; b4055.
DR EnsemblBacteria; BAE78057; BAE78057; BAE78057.
DR GeneID; 58462006; -.
DR GeneID; 948562; -.
DR KEGG; ecj:JW4015; -.
DR KEGG; eco:b4055; -.
DR PATRIC; fig|511145.12.peg.4176; -.
DR EchoBASE; EB1878; -.
DR eggNOG; COG3700; Bacteria.
DR HOGENOM; CLU_081496_0_0_6; -.
DR OMA; PEFWEKM; -.
DR PhylomeDB; P0AE22; -.
DR BioCyc; EcoCyc:APHA-MON; -.
DR BioCyc; MetaCyc:APHA-MON; -.
DR BRENDA; 3.1.3.2; 2026.
DR SABIO-RK; P0AE22; -.
DR EvolutionaryTrace; P0AE22; -.
DR PRO; PR:P0AE22; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0030288; C:outer membrane-bounded periplasmic space; IDA:EcoCyc.
DR GO; GO:0003993; F:acid phosphatase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0036424; F:L-phosphoserine phosphatase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR CDD; cd07499; HAD_CBAP; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR005519; Acid_phosphat_B-like.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR010025; HAD-SF_ppase_IIIB_AphA.
DR InterPro; IPR023214; HAD_sf.
DR Pfam; PF03767; Acid_phosphat_B; 1.
DR PIRSF; PIRSF017818; Acid_Ptase_B; 1.
DR SFLD; SFLDG01127; C1.3:_Acid_Phosphatase_Like; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01672; AphA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Magnesium;
KW Metal-binding; Periplasm; Reference proteome; Signal.
FT SIGNAL 1..25
FT /note="Or 23"
FT /evidence="ECO:0000269|PubMed:9298646"
FT CHAIN 26..237
FT /note="Class B acid phosphatase"
FT /id="PRO_0000024004"
FT ACT_SITE 69
FT /note="Nucleophile"
FT ACT_SITE 71
FT /note="Proton donor"
FT BINDING 69
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 71
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 137..138
FT /ligand="substrate"
FT BINDING 177
FT /ligand="substrate"
FT BINDING 192
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT HELIX 37..41
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:2B82"
FT HELIX 51..57
FT /evidence="ECO:0007829|PDB:2B82"
FT TURN 58..60
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 65..68
FT /evidence="ECO:0007829|PDB:2B82"
FT TURN 72..74
FT /evidence="ECO:0007829|PDB:2B82"
FT HELIX 78..88
FT /evidence="ECO:0007829|PDB:2B82"
FT HELIX 94..97
FT /evidence="ECO:0007829|PDB:2B82"
FT HELIX 99..106
FT /evidence="ECO:0007829|PDB:2B82"
FT HELIX 109..112
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 113..115
FT /evidence="ECO:0007829|PDB:1RMT"
FT HELIX 117..129
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 132..137
FT /evidence="ECO:0007829|PDB:2B82"
FT HELIX 147..154
FT /evidence="ECO:0007829|PDB:2B82"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:1RMT"
FT HELIX 178..183
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 186..193
FT /evidence="ECO:0007829|PDB:2B82"
FT HELIX 194..202
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:2B82"
FT TURN 224..227
FT /evidence="ECO:0007829|PDB:2B82"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:2B82"
FT TURN 233..236
FT /evidence="ECO:0007829|PDB:2B82"
SQ SEQUENCE 237 AA; 26104 MW; 35C1BFE6DF9E530D CRC64;
MRKITQAISA VCLLFALNSS AVALASSPSP LNPGTNVARL AEQAPIHWVS VAQIENSLAG
RPPMAVGFDI DDTVLFSSPG FWRGKKTFSP ESEDYLKNPV FWEKMNNGWD EFSIPKEVAR
QLIDMHVRRG DAIFFVTGRS PTKTETVSKT LADNFHIPAT NMNPVIFAGD KPGQNTKSQW
LQDKNIRIFY GDSDNDITAA RDVGARGIRI LRASNSTYKP LPQAGAFGEE VIVNSEY
