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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Enzyme: pyridoxal phosphatase / fructose 1,6-bisphosphatase



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

Regulation Summary Diagram: ?

Summary:
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]. The phosphatase activity of YbhA was first discovered in a high-throughput screen of purified proteins [Kuznetsova05].

YbhA may exist as a homodimer in solution [Saito06].
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)
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: ?

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred by computational analysis Inferred from experiment [Kuznetsova06, Saito06, GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
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]

Credits:
Last-Curated ? 02-Oct-2006 by Keseler I , SRI International


Enzymatic reaction of: pyridoxal phosphatase

Synonyms: HAD14

EC Number: 3.1.3.74

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 of enzyme catalysis.

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:

Substrate
Km (μM)
Citations
pyridoxal 5'-phosphate
370.0
[Kuznetsova06]


Enzymatic reaction of: fructose 1,6-bisphosphatase

Synonyms: HAD14

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.

Alternative Substrates for fructose 1,6-bisphosphate: 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-6P) , glycolysis I (from glucose-6P)

Cofactors or Prosthetic Groups: Mg2+ [Kuznetsova06]

Kinetic Parameters:

Substrate
Km (μM)
Citations
fructose 1,6-bisphosphate
2400.0
[Kuznetsova06]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 9 -> 11
[UniProt12b]
UniProt: Substrate; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 9
[UniProt10b]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Active-Site 9
[UniProt10b]
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 11
[UniProt10b]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 223
[UniProt10b]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

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

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

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProtGOA11a: 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 18.5 on Mon Dec 22, 2014, BIOCYC13A.