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Escherichia coli K-12 substr. MG1655 Enzyme: 2-deoxyglucose-6-phosphatase



Gene: yniC Accession Numbers: G6932 (EcoCyc), b1727, ECK1725

Regulation Summary Diagram: ?

Summary:
YniC is a sugar phosphatase belonging to the superfamily of haloacid dehalogenase (HAD)-like hydrolases. Its preferred substrate is 2-deoxyglucose-6-phosphate [Kuznetsova06]. The phosphatase activity of YniC was first discovered in a high-throughput screen of purified proteins [Kuznetsova05].

Phosphatase activity of YniC is dependent on the presence of a divalent cation such as Mg2+, which appears to affect substrate binding [Kuznetsova06].

Mutagenesis of the predicted catalytic Asp residues in YniC results in loss of phosphatase activity. A yniC deletion mutant is more sensitive to the presence of 2-deoxyglucose in the growth medium than wild type, while a strain overexpressing yniC tolerates higher concentrations of 2-deoxyglucose [Kuznetsova06]. 2-deoxyglucose is taken up by E. coli and is phosphorylated to 2-deoxyglucose-6P, a toxic analog of glucose-6P [Dietz71].

Locations: cytosol

Map Position: [1,807,404 -> 1,808,072] (38.96 centisomes)
Length: 669 bp / 222 aa

Molecular Weight of Polypeptide: 24.33 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005761 , DIP:DIP-12777N , EchoBASE:EB3744 , EcoGene:EG13988 , EcoliWiki:b1727 , Mint:MINT-1257246 , ModBase:P77247 , OU-Microarray:b1727 , PortEco:yniC , Pride:P77247 , Protein Model Portal:P77247 , RefSeq:NP_416241 , RegulonDB:G6932 , SMR:P77247 , String:511145.b1727 , UniProt:P77247

Relationship Links: InterPro:IN-FAMILY:IPR005833 , InterPro:IN-FAMILY:IPR006402 , InterPro:IN-FAMILY:IPR006439 , InterPro:IN-FAMILY:IPR023198 , InterPro:IN-FAMILY:IPR023214 , PDB:Structure:1TE2 , Pfam:IN-FAMILY:PF00702 , Prints:IN-FAMILY:PR00413

In Paralogous Gene Group: 276 (8 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred by computational analysis Inferred from experiment [Kuznetsova06, GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Kuznetsova06]
GO:0003850 - 2-deoxyglucose-6-phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01, Kuznetsova06]
GO:0004346 - glucose-6-phosphatase activity Inferred from experiment [Kuznetsova06]
GO:0016791 - phosphatase activity Inferred from experiment [Kuznetsova06]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Kuznetsova06]
GO:0050308 - sugar-phosphatase activity Inferred from experiment Inferred by computational analysis [GOA01, Kuznetsova06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: cell processes protection detoxification

Essentiality data for yniC 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:
Last-Curated ? 27-Sep-2006 by Keseler I , SRI International


Enzymatic reaction of: 2-deoxyglucose-6-phosphatase

Synonyms: HAD1

EC Number: 3.1.3.68

2-deoxy-D-glucose 6-phosphate + H2O <=> 2-deoxy-D-glucose + 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 2-deoxy-D-glucose 6-phosphate: β-D-glucose 6-phosphate [Kuznetsova06 ] , D-ribose 5-phosphate [Kuznetsova06 ] , 2-deoxy-D-ribose 5-phosphate [Kuznetsova06 ] , α-D-mannose 6-phosphate [Kuznetsova06 ]

Summary:
Kms for the alternative substrates are in the 2.5-4.7 mM range with Zn2+ as the cofactor [Kuznetsova06].

Cofactors or Prosthetic Groups: Mn2+ [Kuznetsova06]

Kinetic Parameters:

Substrate
Km (μM)
Citations
2-deoxy-D-glucose 6-phosphate
610.0
[Kuznetsova06]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 13
[Kuznetsova06, UniProt12a]
Alternate sequence: D → A; UniProt: Loss of the phosphatase activity.
Metal-Binding-Site 13
[UniProt12a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Active-Site 13
[UniProt12a]
UniProt: Nucleophile.
Protein-Segment 13 -> 15
[UniProt12a]
UniProt: Substrate; Sequence Annotation Type: region of interest.
Metal-Binding-Site 15
[UniProt12a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Protein-Segment 115 -> 116
[UniProt12a]
UniProt: Substrate; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 148
[UniProt12a]
UniProt: Substrate binding.
Metal-Binding-Site 173
[UniProt12a]
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 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

Dietz71: Dietz GW, Heppel LA (1971). "Studies on the uptake of hexose phosphates. I. 2-Deoxyglucose and 2-deoxyglucose 6-phosphate." J Biol Chem 246(9);2881-4. PMID: 4928893

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."

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

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

UniProt12a: 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."

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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 Thu Dec 18, 2014, BIOCYC14A.