Escherichia coli K-12 substr. MG1655 Enzyme: fructose 1,6-bisphosphatase II

Gene: glpX Accession Numbers: EG11517 (EcoCyc), b3925, ECK3917

Synonyms: FBPase II

Regulation Summary Diagram: ?

Regulation summary diagram for glpX

Subunit composition of fructose 1,6-bisphosphatase II = [GlpX]2
         fructose 1,6-bisphosphatase II = GlpX

The glpX gene encodes a Type II fructose 1,6-bisphosphatase (FBPase II). Its enzymatic properties are distinct from those of FBPase I [Donahue00, Brown09].

Crystal structures of free GlpX and GlpX complexed with substrate or inorganic phosphate have been solved; the enzyme forms an elongated dimer in the crystal. A catalytic mechanism has been proposed [Brown09].

When FBPase I is present, FBPase II is not essential for growth; a glpX mutant strain grows normally on gluconeogenic substrates, although increased expression of glpX from a multicopy plasmid complements an Fbp- phenotype [Donahue00]. Enzymes with mutations in predicted active site residues have been isolated, and their enzymatic properties have been measured [Brown09].

The glpX gene was initially identified as a gene of unknown function belonging to the glpFKX operon of the glp regulon [Truniger92, Weissenborn92]. GlpX shares only 10% amino acid sequence identity with FBPase I [Donahue00]. E. coli also has a second Type II FBPase, YggF. GlpX has a catalytic efficiency three times higher than YggF, but a lower catalytic efficiency and substrate affinity than Fbp [Brown09].

In metabolic engineering studies, overexpression of glpX enhanced gluconeogenic flux, activating the pentose phosphate pathway and increasing hydrogen yield in strains of E. coli containing a ferredoxin-dependent hydrogenase system [Kim11b]. Co-overexpression of glpX and tktA improved L-phenylalanine production from glycerol in recombinant E. coli strains [Gottlieb14]. Deletion of glpX strongly increased acrAB expression in wild-type E. coli BW25113, although the cause of the induction remains unclear [Ruiz14].

Gene Citations: [Lupski90]

Locations: cytosol

Map Position: [4,112,592 <- 4,113,602] (88.64 centisomes, 319°)
Length: 1011 bp / 336 aa

Molecular Weight of Polypeptide: 35.852 kD (from nucleotide sequence), 40.0 kD (experimental) [Donahue00 ]

Molecular Weight of Multimer: 80.0 kD (experimental) [Donahue00]

Unification Links: ASAP:ABE-0012821 , CGSC:30884 , EchoBASE:EB1479 , EcoGene:EG11517 , EcoliWiki:B3925 , ModBase:P0A9C9 , OU-Microarray:b3925 , PortEco:glpX , PR:PRO_000022800 , Pride:P0A9C9 , Protein Model Portal:P0A9C9 , RefSeq:NP_418360 , RegulonDB:EG11517 , SMR:P0A9C9 , String:511145.b3925 , UniProt:P0A9C9

Relationship Links: InterPro:IN-FAMILY:IPR004464 , PDB:Structure:1NI9 , PDB:Structure:2R8T , PDB:Structure:3BIG , PDB:Structure:3BIH , PDB:Structure:3D1R , Pfam:IN-FAMILY:PF03320

In Paralogous Gene Group: 100 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for glpX

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Donahue00]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006071 - glycerol metabolic process Inferred by computational analysis [GOA01]
GO:0006094 - gluconeogenesis Inferred by computational analysis [UniProtGOA12, GOA01]
Molecular Function: GO:0030145 - manganese ion binding Inferred from experiment [Donahue00]
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Donahue00]
GO:0042803 - protein homodimerization activity Inferred from experiment [Donahue00]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism

Essentiality data for glpX 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]

Curated 13-Mar-2009 by Keseler I , SRI International
Last-Curated ? 20-May-2015 by Fulcher C , SRI International

Enzymatic reaction of: fructose 1,6-bisphosphatase

EC Number:

fructose 1,6-bisphosphate + H2O <=> β-D-fructofuranose 6-phosphate + phosphate

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.

In Pathways: superpathway of hexitol degradation (bacteria) , superpathway of glycolysis and Entner-Doudoroff , superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass , gluconeogenesis I , glycolysis II (from fructose 6-phosphate) , glycolysis I (from glucose 6-phosphate)

Substrate binding shows positive cooperativity, with a Hill coefficient of ~2.0 [Brown09].

In contrast to [Donahue00], [Brown09] saw no effect of AMP, ADP, PEP, and glycerol 3-phosphate on enzymatic activity.

The enzyme had low activity toward glucose 1,6-bisphosphate. Non-substrates included ribulose 1,5-bisphosphate, fructose 2,6-bisphosphate, and fructose 1-phosphate. Of several divalent ions tested, only Mn2+ served as cofactor. Activity was stimulated 20% by 20 mM KCl [Brown09].

Cofactors or Prosthetic Groups: Mn2+ [Brown09, Donahue00]

Activators (Unknown Mechanism): phosphoenolpyruvate [Donahue00]

Inhibitors (Competitive): phosphate [Brown09, Donahue00]

Inhibitors (Unknown Mechanism): Li+ [Brown09] , ADP [Donahue00]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Vmax (µmol mg-1 min-1)
fructose 1,6-bisphosphate
fructose 1,6-bisphosphate

pH(opt): 7.5-8 [Brown09]

Sequence Features

Protein sequence of fructose 1,6-bisphosphatase II with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 29
[Brown09, UniProt11a]
UniProt: 2.4-fold increase in FBPase activity, and no effect on substrate affinity.
Metal-Binding-Site 33
UniProt: Manganese 1.
Metal-Binding-Site 57
UniProt: Manganese 1.
Mutagenesis-Variant 57
[Brown09, UniProt11a]
UniProt: Strong decrease in FBPase activity.
Mutagenesis-Variant 59
[Brown09, UniProt11a]
UniProt: 5.5-fold decrease in FBPase activity, and 1.4-fold decrease in substrate affinity.
Mutagenesis-Variant 61
[Brown09, UniProt11a]
UniProt: Great decrease in FBPase activity.
Metal-Binding-Site 85
UniProt: Manganese 2.
Mutagenesis-Variant 85
[Brown09, UniProt11a]
UniProt: Great decrease in FBPase activity.
Metal-Binding-Site 88
UniProt: Manganese 2.
Mutagenesis-Variant 88
[Brown09, UniProt11a]
UniProt: Strong decrease in FBPase activity.
Protein-Segment 88 -> 90
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 90
[Brown09, UniProt11a]
UniProt: Strong decrease in FBPase activity.
Amino-Acid-Sites-That-Bind 119
UniProt: Substrate.
Mutagenesis-Variant 119
[Brown09, UniProt11a]
UniProt: Strong decrease in FBPase activity.
Mutagenesis-Variant 164
[Brown09, UniProt11a]
UniProt: Strong decrease in FBPase activity.
Protein-Segment 164 -> 166
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 166
[Brown09, UniProt11a]
UniProt: Strong decrease in FBPase activity.
Mutagenesis-Variant 186
[Brown09, UniProt11a]
UniProt: 5-fold decrease in FBPase activity, and 3-fold decrease in substrate affinity.
Protein-Segment 186 -> 188
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 188
[Brown09, UniProt11a]
UniProt: Great decrease in FBPase activity.
Amino-Acid-Sites-That-Bind 210
UniProt: Substrate; via amide nitrogen.
Metal-Binding-Site 213
UniProt: Manganese 2.
Mutagenesis-Variant 213
[Brown09, UniProt11a]
UniProt: Great decrease in FBPase activity.
Mutagenesis-Variant 235
[Brown09, UniProt11a]
UniProt: Nearly no effect on FBPase activity, and 3-fold decrease in substrate affinity.
Mutagenesis-Variant 239
[Brown09, UniProt11a]
UniProt: 1.3-fold increase in FBPase activity, and 1.4-fold decrease in substrate affinity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3925 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11517; 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

Brown09: Brown G, Singer A, Lunin VV, Proudfoot M, Skarina T, Flick R, Kochinyan S, Sanishvili R, Joachimiak A, Edwards AM, Savchenko A, Yakunin AF (2009). "Structural and biochemical characterization of the type II fructose-1,6-bisphosphatase GlpX from Escherichia coli." J Biol Chem 284(6);3784-92. PMID: 19073594

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

Donahue00: Donahue JL, Bownas JL, Niehaus WG, Larson TJ (2000). "Purification and characterization of glpX-encoded fructose 1, 6-bisphosphatase, a new enzyme of the glycerol 3-phosphate regulon of Escherichia coli." J Bacteriol 2000;182(19);5624-7. PMID: 10986273

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.

Gottlieb14: Gottlieb K, Albermann C, Sprenger GA (2014). "Improvement of L-phenylalanine production from glycerol by recombinant Escherichia coli strains: the role of extra copies of glpK, glpX, and tktA genes." Microb Cell Fact 13(1);96. PMID: 25012491

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

Kim11b: Kim YM, Cho HS, Jung GY, Park JM (2011). "Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant Escherichia coli." Biotechnol Bioeng 108(12);2941-6. PMID: 21732330

Lupski90: Lupski JR, Zhang YH, Rieger M, Minter M, Hsu B, Ooi BG, Koeuth T, McCabe ER (1990). "Mutational analysis of the Escherichia coli glpFK region with Tn5 mutagenesis and the polymerase chain reaction." J Bacteriol 1990;172(10);6129-34. PMID: 2170343

Ruiz14: Ruiz C, Levy SB (2014). "Regulation of acrAB expression by cellular metabolites in Escherichia coli." J Antimicrob Chemother 69(2);390-9. PMID: 24043404

Truniger92: Truniger V, Boos W, Sweet G (1992). "Molecular analysis of the glpFKX regions of Escherichia coli and Shigella flexneri." J Bacteriol 174(21);6981-91. PMID: 1400248

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Weissenborn92: Weissenborn DL, Wittekindt N, Larson TJ (1992). "Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12." J Biol Chem 1992;267(9);6122-31. PMID: 1372899

Other References Related to Gene Regulation

Beisel12: Beisel CL, Updegrove TB, Janson BJ, Storz G (2012). "Multiple factors dictate target selection by Hfq-binding small RNAs." EMBO J 31(8);1961-74. PMID: 22388518

Zhang11f: Zhang Z, Saier MH (2011). "Transposon-mediated adaptive and directed mutations and their potential evolutionary benefits." J Mol Microbiol Biotechnol 21(1-2);59-70. PMID: 22248543

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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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