Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: acid phosphatase / phosphotransferase



Gene: aphA Accession Numbers: EG11934 (EcoCyc), b4055, ECK4047

Synonyms: yjbP, hobH

Regulation Summary Diagram: ?

Subunit composition of acid phosphatase / phosphotransferase = [AphA]4
         AphA monomer = AphA

Summary:
aphA encodes a periplasmic phosphatase/phosphotransferase that has optimal activity at acidic pH.

The purified enzyme is able to dephosphorylate 5' and 3' mononucleotides, 2-deoxy 5' nucleotides, phenylphosphate, glycerol-2-phosphate, ribose-5-phosphate, O-phospho-L-amino acids (O-phospho-L-serine, O-phospho-L-threonine and O-phospho-L-tyrosine) and phytic acid. No activity was observed on ATP, phosphodiesters, glycerol-1-phosphate, glucose-1-phosphate or glucose-6-phosphate. Purified AphA has phosphotransferase activity, catalysing phosphate transfer from p-nitrophenyl phosphate (pNPP) to adenosine or uridine [Thaller97]

The purified enzyme is active on 3' mononucleotides, 3' monodeoxynucleotides, 5' mononucleotides and 5' monodeoxynucleotides. The purifed enzyme is not active on 3', 5'-cyclic AMP, ADP, ATP, NADH or GTP and shows low activity with sugar phosphates and β glycerol phosphate The purified enzyme does not have any phosphomutase activity but can act as a phosphotransferase [Passariello06].

AphA activity is inhibited by EDTA suggesting that it is a metallo-protein [Thaller97, Passariello06].

Purified AphA is a homotetramer [Thaller97]

AphA is found at high abundance in vivo [Link97].

HobH: hemimethylated origin binding [Herrick94]

Locations: periplasmic space

Map Position: [4,267,437 -> 4,268,150] (91.98 centisomes)
Length: 714 bp / 237 aa

Molecular Weight of Polypeptide: 26.104 kD (from nucleotide sequence)

Molecular Weight of Multimer: 101.0 kD (experimental) [Thaller97]

pI: 6.85 [Han13]

Unification Links: ASAP:ABE-0013283 , EchoBASE:EB1878 , EcoGene:EG11934 , EcoliWiki:b4055 , Mint:MINT-1294190 , ModBase:P0AE22 , OU-Microarray:b4055 , PortEco:aphA , PR:PRO_000022108 , Pride:P0AE22 , Protein Model Portal:P0AE22 , RefSeq:NP_418479 , RegulonDB:EG11934 , SMR:P0AE22 , String:511145.b4055 , Swiss-Model:P0AE22 , UniProt:P0AE22

Relationship Links: InterPro:IN-FAMILY:IPR005519 , InterPro:IN-FAMILY:IPR010025 , InterPro:IN-FAMILY:IPR023214 , PDB:Structure:1N8N , PDB:Structure:1N9K , PDB:Structure:1RMQ , PDB:Structure:1RMT , PDB:Structure:1RMY , PDB:Structure:2B82 , PDB:Structure:2B8J , PDB:Structure:2G1A , PDB:Structure:2HEG , PDB:Structure:2HF7 , PDB:Structure:3CZ4 , Pfam:IN-FAMILY:PF03767

Gene-Reaction Schematic: ?

Instance reactions of [a nucleoside 3'-phosphate + H2O → a ribonucleoside + phosphate] (3.1.3.6):
i11: cytidine-3'-monophosphate + H2O → cytidine + phosphate (3.1.3.6)

i12: uridine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → uridine[periplasmic space] + phosphate[periplasmic space] (3.1.3.6)

i13: adenosine 3'-monophosphate + H2O → adenosine + phosphate (3.1.3.6)

i14: guanosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → guanosine[periplasmic space] + phosphate[periplasmic space] (3.1.3.6)

Instance reaction of [a 2'-deoxyribonucleoside 5'-monophosphate + H2O → a 2'-deoxynucleoside + phosphate] (3.1.3.89):
i1: dTMP + H2O → thymidine + phosphate (3.1.3.89)

Instance reaction of [a ribonucleoside 5'-monophosphate + H2O → a ribonucleoside + phosphate] (3.1.3.5):
i4: CMP + H2O → cytidine + phosphate (3.1.3.91)

Instance reactions of [a 2'-deoxyribonucleoside 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → a 2'-deoxynucleoside[periplasmic space] + phosphate[periplasmic space]] (3.1.3.34):
i15: 2'-deoxyadenosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → 2'-deoxyadenosine[periplasmic space] + phosphate[periplasmic space] (3.1.3.34)

i16: thymidine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → thymidine[periplasmic space] + phosphate[periplasmic space] (3.1.3.34)

i17: 2'-deoxyguanosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → 2'-deoxyguanosine[periplasmic space] + phosphate[periplasmic space] (3.1.3.34)

i18: 2'-deoxyuridine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → 2'-deoxyuridine[periplasmic space] + phosphate[periplasmic space] (3.1.3.34)

i19: 2'-deoxycytidine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] → 2'-deoxycytidine[periplasmic space] + phosphate[periplasmic space] (3.1.3.34)

Instance reactions of [a nucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] → a nucleoside[periplasmic space] + phosphate[periplasmic space]] (no EC#):
i2: dAMP + H2O → 2'-deoxyadenosine + phosphate (3.1.3.89)

i3: dCMP + H2O → 2'-deoxycytidine + phosphate (3.1.3.89)

i5: UMP + H2O → uridine + phosphate (3.1.3.5)

i6: dGMP + H2O → 2'-deoxyguanosine + phosphate (3.1.3.89)

i7: GMP + H2O → guanosine + phosphate (3.1.3.5)

i8: IMP + H2O → inosine + phosphate (3.1.3.5)

i9: AMP + H2O → adenosine + phosphate (3.1.3.5)

i10: dUMP + H2O → 2'-deoxyuridine + phosphate (3.1.3.89)

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred by computational analysis Inferred from experiment [Thaller97, Passariello06, GOA01a, GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003993 - acid phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Thaller97, Passariello06]
GO:0004647 - phosphoserine phosphatase activity Inferred from experiment [Thaller97]
GO:0048037 - cofactor binding Inferred from experiment [Thaller97, Calderone04]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [GOA01, DiazMejia09, Han13, Rossolini94]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for aphA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 07-May-2013 by Mackie A , Macquarie University


Enzymatic reaction of: acid phosphatase / phosphotransferase

Synonyms: class B acid phosphatase/phosphotransferase, acid phosphatase, non-specific acid phosphatase, NAP, acid phosphomonoesterase, phosphomonoesterase, glycerophosphatase, orthophosphoric-monoester phosphohydrolase (acid optimum)

EC Number: 3.1.3.2

a phosphate monoester[periplasmic space] + H2O[periplasmic space] <=> an alcohol[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

Alternative Substrates for a phosphate monoester: glycerol 2-phosphate [Thaller97 ] , 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate [Thaller97 ]

Cofactors or Prosthetic Groups: Mg2+ [Comment 5]

Activators (Unknown Mechanism): ethanol [Thaller97]

Inhibitors (Unknown Mechanism): guanosine [Thaller97] , a nucleoside [Thaller97] , Ca2+ [Thaller97] , phosphate [Thaller97] , uridine [Thaller97] , EDTA [Thaller97]

Primary Physiological Regulators of Enzyme Activity: Ca2+ , phosphate , uridine

pH(opt): 6 [Rossolini94]


Enzymatic reaction of: nucleoside monophosphate phosphatase (acid phosphatase / phosphotransferase)

a nucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> a nucleoside[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: adenosine nucleotides degradation II , guanosine nucleotides degradation III


Enzymatic reaction of: nucleoside 5'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.5

a ribonucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> a ribonucleoside[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: adenosine nucleotides degradation II , guanosine nucleotides degradation III


Enzymatic reaction of: nucleoside 3'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.6

a nucleoside 3'-phosphate[periplasmic space] + H2O[periplasmic space] <=> a ribonucleoside[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: 2'-deoxyribonucleoside 5'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.89

a 2'-deoxyribonucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> a 2'-deoxynucleoside[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.


Enzymatic reaction of: 2'-deoxyribonucleoside 3'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.34

a 2'-deoxyribonucleoside 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> a 2'-deoxynucleoside[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.


Enzymatic reaction of: 2'-deoxycytidine 3'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.34

2'-deoxycytidine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> 2'-deoxycytidine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
2'-deoxycytidine 3'-monophosphate
1.3
[Passariello06]


Enzymatic reaction of: 2'-deoxyguanosine 3'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.34

2'-deoxyguanosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> 2'-deoxyguanosine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
2'-deoxyguanosine 3'-monophosphate
1.6
[Passariello06]


Enzymatic reaction of: 2'-deoxyuridine 3'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.34

2'-deoxyuridine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> 2'-deoxyuridine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
2'-deoxyuridine 3'-monophosphate
0.9
[Passariello06]


Enzymatic reaction of: 2'-deoxyadenosine 3'-monophosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.34

2'-deoxyadenosine 3'-monophosphate[periplasmic space] + H2O[periplasmic space] <=> 2'-deoxyadenosine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
2'-deoxyadenosine 3'-monophosphate
1.5
[Passariello06]


Enzymatic reaction of: L-threonine O-3-phosphate phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.-

L-threonine 3-O-phosphate[periplasmic space] + H2O[periplasmic space] <=> L-threonine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.


Enzymatic reaction of: 3-phosphoserine phosphatase (acid phosphatase / phosphotransferase)

EC Number: 3.1.3.3

3-phospho-L-serine[periplasmic space] + H2O[periplasmic space] <=> L-serine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.


Enzymatic reaction of: O-phospho-L-tyrosine phosphatase (acid phosphatase / phosphotransferase)

O-phospho-L-tyrosine[periplasmic space] + H2O[periplasmic space] <=> L-tyrosine[periplasmic space] + phosphate[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 25
[Link97, UniProt11a]
UniProt: Or 23.
Chain 26 -> 237
[UniProt09]
UniProt: Class B acid phosphatase;
Active-Site 69
[UniProt12]
UniProt: Nucleophile.
Metal-Binding-Site 69
[UniProt10]
UniProt: Magnesium;
Active-Site 71
[UniProt12]
UniProt: Proton donor.
Metal-Binding-Site 71
[UniProt10]
UniProt: Magnesium; via carbonyl oxygen;
Protein-Segment 137 -> 138
[UniProt12]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 177
[UniProt12]
UniProt: Substrate.
Metal-Binding-Site 192
[UniProt10]
UniProt: Magnesium;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4055 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11934; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Calderone04: Calderone V, Forleo C, Benvenuti M, Cristina Thaller M, Maria Rossolini G, Mangani S (2004). "The first structure of a bacterial class B Acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold." J Mol Biol 335(3);761-73. PMID: 14687572

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Han13: Han MJ, Kim JY, Kim JA (2013). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng. PMID: 24140104

Herrick94: Herrick J, Kern R, Guha S, Landoulsi A, Fayet O, Malki A, Kohiyama M (1994). "Parental strand recognition of the DNA replication origin by the outer membrane in Escherichia coli." EMBO J 13(19);4695-703. PMID: 7925311

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Passariello06: Passariello C, Forleo C, Micheli V, Schippa S, Leone R, Mangani S, Thaller MC, Rossolini GM (2006). "Biochemical characterization of the class B acid phosphatase (AphA) of Escherichia coli MG1655." Biochim Biophys Acta 1764(1);13-9. PMID: 16297670

Rossolini94: Rossolini GM, Thaller MC, Pezzi R, Satta G (1994). "Identification of an Escherichia coli periplasmic acid phosphatase containing of a 27 kDa-polypeptide component." FEMS Microbiol Lett 118(1-2);167-73. PMID: 8013875

Thaller97: Thaller MC, Schippa S, Bonci A, Cresti S, Rossolini GM (1997). "Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product." FEMS Microbiol Lett 1997;146(2);191-8. PMID: 9011040

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, BIOCYC14B.