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



Gene: yggF Accession Numbers: EG11245 (EcoCyc), b2930, ECK2926

Synonyms: yggK

Regulation Summary Diagram: ?

Regulation summary diagram for yggF

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

Summary:
YggF is a type II fructose-1,6-bisphosphatase and shows 58% sequence identity to GlpX [Brown09].

Genomic SELEX screening predicted a number of novel target genes, including yggF, to be under the control of transcriptional activator cAMP-CRP. The data suggested that CRP has a major role in control of the switch between glycolysis and gluconeogenesis [Shimada11a]. Genomic SELEX screening is described in [Gold95].

Locations: cytosol

Map Position: [3,073,239 <- 3,074,204] (66.24 centisomes, 238°)
Length: 966 bp / 321 aa

Molecular Weight of Polypeptide: 34.323 kD (from nucleotide sequence)

Molecular Weight of Multimer: 76.0 kD (experimental) [Brown09]

Unification Links: ASAP:ABE-0009615 , EchoBASE:EB1226 , EcoGene:EG11245 , EcoliWiki:b2930 , ModBase:P21437 , OU-Microarray:b2930 , PortEco:yggF , Protein Model Portal:P21437 , RefSeq:NP_417405 , RegulonDB:EG11245 , SMR:P21437 , String:511145.b2930 , Swiss-Model:P21437 , UniProt:P21437

Relationship Links: InterPro:IN-FAMILY:IPR004464 , Pfam:IN-FAMILY:PF03320

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Brown09]
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 [GOA01]
Molecular Function: GO:0030145 - manganese ion binding Inferred from experiment [Brown09]
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Brown09]
GO:0042803 - protein homodimerization activity Inferred from experiment [Brown09]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism

Essentiality data for yggF 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]

Credits:
Created 13-Mar-2009 by Keseler I , SRI International
Curated 13-Mar-2009 by Keseler I , SRI International
Last-Curated ? 21-May-2015 by Fulcher C , 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 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)

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

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 [Brown09].

Addition of 1 mM dithiothreitol increased the activity 40-50%, whereas 1 mM ATP reduced the activity by 40%. Addition of 1 mM AMP, ADP, PEP, and glycerol 3-phosphate had no significant effect on activity [Brown09].

Cofactors or Prosthetic Groups: Mn2+ [Brown09]

Activators (Unknown Mechanism): L-dithiothreitol [Brown09]

Inhibitors (Unknown Mechanism): ATP [Brown09] , potassium chloride [Brown09] , Li+ [Brown09] , phosphate [Brown09]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
fructose 1,6-bisphosphate
100.0
2.5
0.025
[Brown09, BRENDA14]

pH(opt): 7.5-8 [Brown09]


Sequence Features

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

Feature Class Location Citations Comment
Metal-Binding-Site 32
[UniProt11]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 56
[UniProt11]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 84
[UniProt11]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 87
[UniProt11]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity.
Protein-Segment 87 -> 89
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 118
[UniProt11]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Protein-Segment 163 -> 165
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 182 -> 186
[Alefounder89, UniProt10a]
UniProt: (in Ref. 3);
Protein-Segment 185 -> 187
[UniProt11]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 209
[UniProt11]
UniProt: Substrate; via amide nitrogen; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 212
[UniProt11]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b2930 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11245; confirmed by SwissProt match.


References

Alefounder89: Alefounder PR, Perham RN (1989). "Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli." Mol Microbiol 3(6);723-32. PMID: 2546007

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

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

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.

Gold95: Gold L, Polisky B, Uhlenbeck O, Yarus M (1995). "Diversity of oligonucleotide functions." Annu Rev Biochem 64;763-97. PMID: 7574500

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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Shimada11a: Shimada T, Fujita N, Yamamoto K, Ishihama A (2011). "Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources." PLoS One 6(6);e20081. PMID: 21673794

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.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords 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 19.0 on Thu Jul 30, 2015, biocyc14.