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

Gene: ybhA Accession Numbers: EG11239 (EcoCyc), b0766, ECK0755

Regulation Summary Diagram: ?

Regulation summary diagram for ybhA

YbhA is a promiscuous phosphatase belonging to the superfamily of haloacid dehalogenase (HAD)-like hydrolases. Its preferred substrates are pyridoxal phosphate and fructose 1,6-bisphosphate [Kuznetsova06]. In addition, YbhA appears to have a low level of phosphotransferase activity using monophosphates as the phosphate donor [Saito06] and a low β-phosphoglucomutase activity [Kuznetsova06]. The phosphatase activity of YbhA was first discovered in a high-throughput screen of purified proteins [Kuznetsova05].

The phosphatase and phosphotransferase activities of YbhA toward different sugars and sugar phosphates were demonstrated using enzyme assays and metabolic profiling by capillary electrophoresis-mass spectrometry (CE-MS). Relative to its phosphatase activity, YbhA showed very low phosphotransferase activity as detected by CE-MS assay using glycerol as substrate and inorganic phosphate as donor. Other phosphate donors included the monophosphates AMP, ribose-5-phosphate, and glucose-6-phosphate, whereas nucleotide di- and triphosphates could not act as donor [Saito06].

YbhA may exist as a homodimer in solution based on gel filtration analysis of purified recombinant protein which showed the presence of both a monomer and a homodimer [Saito06].

Compared with the Fbp, GlpX, YggF and YaeD fructose 1,6-bisphosphate phosphatases from E. coli, YbhA was less efficient than Fbp, GlpX and YggF in hydrolysis of fructose 1,6-bisphosphate [Brown09].
An open reading frame downstream of and in the same orientation as modABC, modD, was originally annotated at this location [Rech95].

Locations: cytosol

Map Position: [796,836 <- 797,654] (17.17 centisomes, 62°)
Length: 819 bp / 272 aa

Molecular Weight of Polypeptide: 30.201 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002607 , CGSC:37794 , EchoBASE:EB1221 , EcoGene:EG11239 , EcoliWiki:b0766 , ModBase:P21829 , OU-Microarray:b0766 , PortEco:ybhA , Protein Model Portal:P21829 , RefSeq:NP_415287 , RegulonDB:EG11239 , SMR:P21829 , String:511145.b0766 , UniProt:P21829

Relationship Links: InterPro:IN-FAMILY:IPR000150 , InterPro:IN-FAMILY:IPR006379 , InterPro:IN-FAMILY:IPR023214 , Pfam:IN-FAMILY:PF00702 , Prosite:IN-FAMILY:PS01228 , Prosite:IN-FAMILY:PS01229

In Paralogous Gene Group: 129 (5 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0016311 - dephosphorylation Inferred by computational analysis [Gaudet10]
GO:0044283 - small molecule biosynthetic process Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Kuznetsova06]
GO:0016773 - phosphotransferase activity, alcohol group as acceptor Inferred from experiment [Saito06]
GO:0016791 - phosphatase activity Inferred from experiment [Kuznetsova06]
GO:0033883 - pyridoxal phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01, Kuznetsova06]
GO:0050308 - sugar-phosphatase activity Inferred from experiment [Kuznetsova06, Saito06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]

MultiFun Terms: metabolism central intermediary metabolism pyridoxal 5'-phosphate salvage
metabolism central intermediary metabolism

Essentiality data for ybhA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Curated 02-Oct-2006 by Keseler I , SRI International
Last-Curated ? 26-May-2015 by Fulcher C , SRI International

Enzymatic reaction of: pyridoxal phosphatase

Synonyms: HAD14

EC Number:

pyridoxal 5'-phosphate + H2O <=> pyridoxal + 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.

Alternative Substrates for pyridoxal 5'-phosphate: imidodiphosphate [Kuznetsova06 ]

Cofactors or Prosthetic Groups: Mg2+ [Kuznetsova06]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
pyridoxal 5'-phosphate

Enzymatic reaction of: fructose 1,6-bisphosphatase

Synonyms: HAD14

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.

Alternative Substrates for fructose 1,6-bisphosphate: acetyl phosphate [Kuznetsova06 ] , D-ribose 5-phosphate [Saito06 ] , D-glucose 6-phosphate [Saito06 ] , sn-glycerol 3-phosphate [Saito06 ] , imidodiphosphate [Kuznetsova06 ] , D-erythrose 4-phosphate [Kuznetsova06 ]

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)

Cofactors or Prosthetic Groups: Mg2+ [Kuznetsova06]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
fructose 1,6-bisphosphate

Sequence Features

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

Feature Class Location Citations Comment
Metal-Binding-Site 9
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Active-Site 9
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 10
UniProt: Phosphate; via amide nitrogen.
Metal-Binding-Site 11
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Protein-Segment 43 -> 44
UniProt: Phosphate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 200
UniProt: Phosphate.
Metal-Binding-Site 223
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 226
UniProt: Phosphate.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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 b0766 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11239; 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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kuznetsova05: Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF (2005). "Enzyme genomics: Application of general enzymatic screens to discover new enzymes." FEMS Microbiol Rev 29(2);263-79. PMID: 15808744

Kuznetsova06: Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF (2006). "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family." J Biol Chem 281(47):36149-61. PMID: 16990279

Rech95: Rech S, Deppenmeier U, Gunsalus RP (1995). "Regulation of the molybdate transport operon, modABCD, of Escherichia coli in response to molybdate availability." J Bacteriol 177(4);1023-9. PMID: 7860583

Saito06: Saito N, Robert M, Kitamura S, Baran R, Soga T, Mori H, Nishioka T, Tomita M (2006). "Metabolomics approach for enzyme discovery." J Proteome Res 5(8);1979-87. PMID: 16889420

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

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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 Tue Oct 6, 2015, biocyc13.