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: fructose 1,6-bisphosphatase II



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

Synonyms: FBPase II

Regulation Summary Diagram: ?

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

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

Crystal structures of free and complexed GlpX 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 [Donahue00]. Enzymes with mutations in predicted active site residues have been isolated, and their enzymatic properties have been measured [Brown09].

Gene Citations: [Lupski90, Weissenborn92, Truniger92]

Locations: cytosol

Map Position: [4,112,592 <- 4,113,602] (88.64 centisomes)
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: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred by computational analysis Inferred from experiment [Donahue00, GOA01, GOA01a]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006071 - glycerol metabolic process Inferred by computational analysis [GOA01a]
GO:0006094 - gluconeogenesis Inferred by computational analysis [UniProtGOA12, GOA01a]
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 [GOA01, GOA01a, Donahue00]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
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]

Credits:
Last-Curated ? 13-Mar-2009 by Keseler I , SRI International


Enzymatic reaction of: fructose 1,6-bisphosphatase

EC Number: 3.1.3.11

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 of enzyme catalysis.

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-6P) , glycolysis I (from glucose-6P)

Summary:
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.

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:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
fructose 1,6-bisphosphate
2.0
[Babul83, BRENDA14]
fructose 1,6-bisphosphate
35.0
[Donahue00]
fructose 1,6-bisphosphate
100.0
2.5
[Brown09, BRENDA14]

pH(opt): 7.5 [BRENDA14, Brown09], 7.8 [BRENDA14, KelleyLoughnane02], 7.5-8 [Brown09]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 29
[Brown09, UniProt11]
Alternate sequence: K → A; UniProt: 2.4-fold increase in FBPase activity, and no effect on substrate affinity.
Metal-Binding-Site 33
[UniProt11]
UniProt: Manganese 1.
Mutagenesis-Variant 57
[Brown09, UniProt11]
Alternate sequence: E → A; UniProt: Strong decrease in FBPase activity.
Metal-Binding-Site 57
[UniProt11]
UniProt: Manganese 1.
Mutagenesis-Variant 59
[Brown09, UniProt11]
Alternate sequence: E → A; UniProt: 5.5-fold decrease in FBPase activity, and 1.4-fold decrease in substrate affinity.
Mutagenesis-Variant 61
[Brown09, UniProt11]
Alternate sequence: D → A; UniProt: Great decrease in FBPase activity.
Mutagenesis-Variant 85
[Brown09, UniProt11]
Alternate sequence: D → A; UniProt: Great decrease in FBPase activity.
Metal-Binding-Site 85
[UniProt11]
UniProt: Manganese 2.
Mutagenesis-Variant 88
[Brown09, UniProt11]
Alternate sequence: E → A; UniProt: Strong decrease in FBPase activity.
Metal-Binding-Site 88
[UniProt11]
UniProt: Manganese 2.
Protein-Segment 88 -> 90
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 90
[Brown09, UniProt11]
Alternate sequence: T → A; UniProt: Strong decrease in FBPase activity.
Mutagenesis-Variant 119
[Brown09, UniProt11]
Alternate sequence: Y → A; UniProt: Strong decrease in FBPase activity.
Amino-Acid-Sites-That-Bind 119
[UniProt11]
UniProt: Substrate.
Mutagenesis-Variant 164
[Brown09, UniProt11]
Alternate sequence: K → A; UniProt: Strong decrease in FBPase activity.
Protein-Segment 164 -> 166
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 166
[Brown09, UniProt11]
Alternate sequence: R → A; UniProt: Strong decrease in FBPase activity.
Mutagenesis-Variant 186
[Brown09, UniProt11]
Alternate sequence: D → A; UniProt: 5-fold decrease in FBPase activity, and 3-fold decrease in substrate affinity.
Protein-Segment 186 -> 188
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 188
[Brown09, UniProt11]
Alternate sequence: D → A; UniProt: Great decrease in FBPase activity.
Amino-Acid-Sites-That-Bind 210
[UniProt11]
UniProt: Substrate; via amide nitrogen.
Mutagenesis-Variant 213
[Brown09, UniProt11]
Alternate sequence: E → A; UniProt: Great decrease in FBPase activity.
Metal-Binding-Site 213
[UniProt11]
UniProt: Manganese 2.
Mutagenesis-Variant 235
[Brown09, UniProt11]
Alternate sequence: R → A; UniProt: Nearly no effect on FBPase activity, and 3-fold decrease in substrate affinity.
Mutagenesis-Variant 239
[Brown09, UniProt11]
Alternate sequence: K → A; UniProt: 1.3-fold increase in FBPase activity, and 1.4-fold decrease in substrate affinity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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

Babul83: Babul J, Guixe V (1983). "Fructose bisphosphatase from Escherichia coli. Purification and characterization." Arch Biochem Biophys 1983;225(2);944-9. PMID: 6312898

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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, 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."

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

KelleyLoughnane02: Kelley-Loughnane N, Biolsi SA, Gibson KM, Lu G, Hehir MJ, Phelan P, Kantrowitz ER (2002). "Purification, kinetic studies, and homology model of Escherichia coli fructose-1,6-bisphosphatase." Biochim Biophys Acta 1594(1);6-16. PMID: 11825604

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

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

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

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

Zhang11d: 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


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 Fri Nov 21, 2014, biocyc14.