Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015

Escherichia coli K-12 substr. MG1655 Enzyme: 3-phytase / glucose-1-phosphatase

Gene: agp Accession Numbers: EG10033 (EcoCyc), b1002, ECK0993

Regulation Summary Diagram: ?

Subunit composition of 3-phytase / glucose-1-phosphatase = [Agp]2

Glucose-1-phosphatase encoded by gene agp is a homodimeric, periplasmic protein. It hydrolyzes phosphate from α-D-glucose-1-phosphate and from 1D-myo-inositol-hexakisphosphate (phytate), hydrolyzing the former substrate with highest efficiency. The enzyme is a member of the histidine acid phosphatase family. It is related to the product of gene appA in reaction mechanism and folding architecture, but not in amino acid sequence.. Their stereospecificity for 1D-myo-inositol-hexakisphosphate hydrolysis also differs. The two-step reaction mechanism involves nucleophilic attack by the conserved histidine residue on the scissile phosphate and subsequent hydrolysis of the phosphohistidine intermediate. AppA sequentially hydrolyzes five of six phosphates beginning with phosphate at the 6 position of the inositol ring. Agp has been shown to hydrolyze only phosphate at the 3 position of 1D-myo-inositol-hexakisphosphate. Agp is believed to function as a scavenger of glucose from α-D-glucose-1-phosphate (in [Cottrill02]).

The crystal structure of this enzyme containing an active site H18A mutation in an inactive complex with α-D-glucose-1-phosphate has been determined at 2.4 Å resolution. It is of interest due to its potential involvement in inositol phosphate signal transduction pathways of pathogens [Lee03d].

The apparent molecular mass of the homodimer was determined by gel filtration chromatography [Pradel88]. The apparent molecular mass of the subunit was determined by SDS-PAGE [Cottrill02, Pradel88]. By MALDI-TOF mass spectrometry its molecular mass was 43.903 kDa [Cottrill02].

Gene Citations: [Pradel89, Pradel90]

Locations: periplasmic space

Map Position: [1,064,808 -> 1,066,049] (22.95 centisomes)
Length: 1242 bp / 413 aa

Molecular Weight of Polypeptide: 45.683 kD (from nucleotide sequence)

Molecular Weight of Multimer: 95.0 kD (experimental) [Pradel88]

pI: 5.4 [Cottrill02]

Unification Links: ASAP:ABE-0003388 , CGSC:31830 , DIP:DIP-2905N , EchoBASE:EB0032 , EcoGene:EG10033 , EcoliWiki:b1002 , ModBase:P19926 , OU-Microarray:b1002 , PortEco:agp , PR:PRO_000022069 , Pride:P19926 , Protein Model Portal:P19926 , RefSeq:NP_415522 , RegulonDB:EG10033 , SMR:P19926 , String:511145.b1002 , UniProt:P19926

Relationship Links: InterPro:IN-FAMILY:IPR000560 , PDB:Structure:1NT4 , Pfam:IN-FAMILY:PF00328 , Prosite:IN-FAMILY:PS00616 , Prosite:IN-FAMILY:PS00778

In Paralogous Gene Group: 234 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006006 - glucose metabolic process Inferred from experiment [Pradel91]
GO:0016311 - dephosphorylation Inferred by computational analysis Inferred from experiment [Cottrill02, GOA01, GOA01a]
Molecular Function: GO:0008877 - glucose-1-phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01, Cottrill02]
GO:0016158 - 3-phytase activity Inferred from experiment [Cottrill02]
GO:0042803 - protein homodimerization activity Inferred from experiment [Pradel88]
GO:0003993 - acid phosphatase activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05, Han13, Pradel88]
GO:0042597 - periplasmic space Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Pradel88]

MultiFun Terms: metabolism central intermediary metabolism misc. glucose metabolism

Essentiality data for agp 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]

Last-Curated ? 17-Mar-2010 by Fulcher C , SRI International

Enzymatic reaction of: 3-phytase

Synonyms: myo-inositol-hexakisphosphate 3-phosphohydrolase, phytase, phytate 1-phosphatase, phytate 6-phosphatase, 1-phytase

EC Number:

1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate[periplasmic space] + H2O[periplasmic space] <=> D-myo-inositol (1,2,4,5,6)-pentakisphosphate[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.

The reaction is physiologically favored in the direction shown. [Cottrill02]

Alternative Substrates for 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate: O-phospho-L-tyrosine [Cottrill02 ] , sn-glycerol 3-phosphate [Cottrill02 ] , β-D-fructofuranose 6-phosphate [Cottrill02 ] , D-ribose 5-phosphate [Cottrill02 ] , β-D-glucose 6-phosphate [Cottrill02 ] , β-D-fructofuranose 1-phosphate [Cottrill02 ] , α-D-glucose 1-phosphate [Cottrill02 ] , 4-nitrophenyl phosphate [Cottrill02 ] , 1D-myo-inositol (1,2,3,4,6)-pentakisphosphate [Cottrill02 ] , D-myo-inositol (1,2,3,4,5)-pentakisphosphate [Cottrill02 ] , D-myo-inositol 1,3,4,5,6-pentakisphosphate [Cottrill02 ]

The enzyme was shown to have a rather broad substrate specificity [Cottrill02].

Kinetic Parameters:

Km (μM)
1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate

T(opt): 60 °C [Cottrill02]

pH(opt): 4.5 [Cottrill02]

Enzymatic reaction of: glucose-1-phosphatase

Synonyms: G1Pase, D-glucose-1-phosphate phosphohydrolase

EC Number:

α-D-glucose 1-phosphate[periplasmic space] + H2O[periplasmic space] <=> D-glucopyranose[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.

The reaction is physiologically favored in the direction shown. [Cottrill02]

The enzyme is most active toward α-D-glucose-1-phosphate as substrate. The pH optimum varies with substrate [Cottrill02].

Kinetic Parameters:

Km (μM)
α-D-glucose 1-phosphate

T(opt): 55 °C [Cottrill02]

pH(opt): 6.5 [Cottrill02]

Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 22
[Pradel90, Link97, UniProt11]
Chain 23 -> 413
UniProt: Glucose-1-phosphatase;
Amino-Acid-Sites-That-Bind 39
UniProt: Substrate.
Active-Site 40
UniProt: Nucleophile;
Amino-Acid-Sites-That-Bind 43
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 116
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 218
UniProt: Substrate.
Protein-Segment 311 -> 313
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Active-Site 312
UniProt: Proton donor;

Gene Local Context (not to scale): ?

Transcription Unit:


10/20/97 Gene b1002 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10033; confirmed by SwissProt match.


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

Cottrill02: Cottrill MA, Golovan SP, Phillips JP, Forsberg CW (2002). "Inositol phosphatase activity of the Escherichia coli agp-encoded acid glucose-1-phosphatase." Can J Microbiol 48(9);801-9. PMID: 12455612

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

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

Lee03d: Lee DC, Cottrill MA, Forsberg CW, Jia Z (2003). "Functional insights revealed by the crystal structures of Escherichia coli glucose-1-phosphatase." J Biol Chem 278(33);31412-8. PMID: 12782623

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Pradel88: Pradel E, Boquet PL (1988). "Acid phosphatases of Escherichia coli: molecular cloning and analysis of agp, the structural gene for a periplasmic acid glucose phosphatase." J Bacteriol 170(10);4916-23. PMID: 2844729

Pradel89: Pradel E, Boquet PL (1989). "Mapping of the Escherichia coli acid glucose-1-phosphatase gene agp and analysis of its expression in vivo by use of an agp-phoA protein fusion." J Bacteriol 171(6);3511-7. PMID: 2542226

Pradel90: Pradel E, Marck C, Boquet PL (1990). "Nucleotide sequence and transcriptional analysis of the Escherichia coli agp gene encoding periplasmic acid glucose-1-phosphatase." J Bacteriol 1990;172(2);802-7. PMID: 2153660

Pradel91: Pradel E, Boquet PL (1991). "Utilization of exogenous glucose-1-phosphate as a source of carbon or phosphate by Escherichia coli K12: respective roles of acid glucose-1-phosphatase, hexose-phosphate permease, phosphoglucomutase and alkaline phosphatase." Res Microbiol 1991;142(1);37-45. PMID: 1648777

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

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

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

Other References Related to Gene Regulation

MedinaRivera11: Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J (2011). "Theoretical and empirical quality assessment of transcription factor-binding motifs." Nucleic Acids Res 39(3);808-24. PMID: 20923783

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 Mar 2, 2015, biocyc13.