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



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

Regulation Summary Diagram: ?

Regulation summary diagram for agp

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

Summary:
Glucose-1-phosphatase (Agp) hydrolyzes phosphate from glucose-1-phosphate and from 1D-myo-inositol-hexakisphosphate (phytate), hydrolyzing the former substrate with highest efficiency [Pradel88, Cottrill02]. Agp functions as a scavenger of glucose from glucose-1-phosphate [Pradel89].

Agp is a member of the histidine acid phosphatase family. It is related to AppA in reaction mechanism and folding architecture, but their specificity for 1D-myo-inositol-hexakisphosphate hydrolysis differs. Agp has been shown to hydrolyze phosphate only at the D-3 position of 1D-myo-inositol-hexakisphosphate. In contrast, AppA sequentially hydrolyzes five of six phosphates beginning with phosphate at the 6 position of the inositol ring [Cottrill02, Lee03d].

Agp from an E. coli B strain (98% identical to the K-12 protein) also functions as a phosphotransferase, transfering the phosphate group to another sugar molecule instead of water. The reaction proceeds via the canonical phosphomonoester hydrolase mechanism, which involves breakage of the P-O bond, not the C1-O bond [Wildberger14].

Agp is a homodimeric protein that resides in the periplasm [Pradel88]. The enzyme was crystallized, and a crystal structure of an active site H18A mutant in an inactive complex with glucose-1-phosphate has been determined at 2.4 Å resolution [Jia01, Lee03d]. The structure shows three consecutive disulfide bonds [Lee03d]; enzymatic activity is dependent on DsbA, but not on DsbC [Berkmen05].

In high-phosphate medium, agp is required for growth on glucose-1-phosphate as the sole source of carbon [Pradel89, Pradel91].

Agp: "periplasmic acid glucose-1-phosphatase" [Pradel88]

Citations: [Dassa90, Belin94, Golovan00]

Gene Citations: [Pradel90]

Locations: periplasmic space

Map Position: [1,064,808 -> 1,066,049] (22.95 centisomes, 83°)
Length: 1242 bp / 413 aa

Molecular Weight of Polypeptide: 45.683 kD (from nucleotide sequence), 44.0 kD (experimental) [Pradel88 ]

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 , InterPro:IN-FAMILY:IPR029033 , 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: ?

Gene-Reaction Schematic

Instance reaction of [a sugar phosphate + H2O → a sugar + phosphate] (3.1.3.23):
i1: α-D-glucopyranose 1-phosphate + H2O → D-glucopyranose + phosphate (3.1.3.10)

Genetic Regulation Schematic: ?

Genetic regulation schematic for agp

GO Terms:

Biological Process: GO:0006007 - glucose catabolic process Inferred from experiment [Pradel89, Pradel91]
GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Cottrill02]
Molecular Function: GO:0008877 - glucose-1-phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01a, 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 [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis Inferred from experiment [Pradel88, DiazMejia09, LopezCampistrou05, Han14]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

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]

Credits:
Curated 17-Mar-2010 by Fulcher C , SRI International
Last-Curated ? 23-Dec-2014 by Keseler I , SRI International


Enzymatic reaction of: glucose-1-phosphatase

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

EC Number: 3.1.3.10

α-D-glucopyranose 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 in which it was curated.

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

Alternative Substrates for H2O: glucose [Wildberger14 ]

Summary:
The enzyme is most active toward α-D-glucose-1-phosphate as substrate. The pH optimum varies with substrate [Cottrill02]. In a transphosphorylase reaction, the enzyme can utilize glucose or fructose as the phosphate acceptor in place of water, producing glucose-6-phosphate or fructose-1-phosphate [Wildberger14].

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
α-D-glucopyranose 1-phosphate
390.0
117.0
0.3
[Cottrill02]

T(opt): 55 °C [Cottrill02]

pH(opt): 6.5 [Cottrill02]


Enzymatic reaction of: 3-phytase (glucose-1-phosphatase)

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

EC Number: 3.1.3.8

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 in which it was curated.

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-glucopyranose 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 ]

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

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate
540.0
12.0
0.022
[Cottrill02]

T(opt): 60 °C [Cottrill02]

pH(opt): 4.5 [Cottrill02]


Sequence Features

Protein sequence of glucose-1-phosphatase with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 22
[Pradel90, Link97, UniProt11, Pradel90]
.
Chain 23 -> 413
[UniProt09]
UniProt: Glucose-1-phosphatase;
Amino-Acid-Sites-That-Bind 39
[UniProt15]
UniProt: Substrate.
Active-Site 40
[UniProt15]
UniProt: Nucleophile.
Amino-Acid-Sites-That-Bind 43
[UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 116
[UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 218
[UniProt15]
UniProt: Substrate.
Protein-Segment 311 -> 313
[UniProt12a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Active-Site 312
[UniProt15]
UniProt: Proton donor.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b1002 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10033; 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

Belin94: Belin P, Quemeneur E, Boquet PL (1994). "A pleiotropic acid phosphatase-deficient mutant of Escherichia coli shows premature termination in the dsbA gene. Use of dsbA::phoA fusions to localize a structurally important domain in DsbA." Mol Gen Genet 242(1);23-32. PMID: 8277944

Berkmen05: Berkmen M, Boyd D, Beckwith J (2005). "The nonconsecutive disulfide bond of Escherichia coli phytase (AppA) renders it dependent on the protein-disulfide isomerase, DsbC." J Biol Chem 280(12);11387-94. PMID: 15642731

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

Dassa90: Dassa J, Marck C, Boquet PL (1990). "The complete nucleotide sequence of the Escherichia coli gene appA reveals significant homology between pH 2.5 acid phosphatase and glucose-1-phosphatase." J Bacteriol 172(9);5497-500. PMID: 2168385

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.

Golovan00: Golovan S, Wang G, Zhang J, Forsberg CW (2000). "Characterization and overproduction of the Escherichia coli appA encoded bifunctional enzyme that exhibits both phytase and acid phosphatase activities." Can J Microbiol 2000;46(1);59-71. PMID: 10696472

Han14: Han MJ, Kim JY, Kim JA (2014). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng 117(4);437-42. PMID: 24140104

Jia01: Jia Z, Cottrill M, Pal GP, Lee D, Sung M, Forsberg CW, Phillips JP (2001). "Purification, crystallization and preliminary X-ray analysis of the Escherichia coli glucose-1-phosphatase." Acta Crystallogr D Biol Crystallogr 57(Pt 2);314-6. PMID: 11173491

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.

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.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

Wildberger14: Wildberger P, Pfeiffer M, Brecker L, Rechberger GN, Birner-Gruenberger R, Nidetzky B (2014). "Phosphoryl transfer from α-d-glucose 1-phosphate catalyzed by Escherichia coli sugar-phosphate phosphatases of two protein-superfamily types." Appl Environ Microbiol. PMID: 25527541

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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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