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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
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Escherichia coli K-12 substr. MG1655 Enzyme: galactitol-1-phosphate dehydrogenase



Gene: gatD Accession Numbers: EG12417 (EcoCyc), b2091, ECK2084

Regulation Summary Diagram: ?

Summary:
Some strains of E. coli K-12 are able to utilize galactitol as the sole source of carbon. After transport into the cell by a specific enzyme II of the PTS, galactitol-1-phosphate dehydrogenase converts galactitol-1-phosphate into tagatose-6-phosphate [Lengeler75, Lengeler77].

Mutants lacking galactitol-1-phosphate dehydrogenase are unable to grow on galactitol [Lengeler77].

Gene Citations: [Nobelmann95, Nobelmann96]

Locations: cytosol

Map Position: [2,169,857 <- 2,170,897] (46.77 centisomes)
Length: 1041 bp / 346 aa

Molecular Weight of Polypeptide: 37.39 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006924 , CGSC:713 , DIP:DIP-47890N , EchoBASE:EB2316 , EcoGene:EG12417 , EcoliWiki:b2091 , Mint:MINT-8389742 , ModBase:P0A9S3 , OU-Microarray:b2091 , PortEco:gatD , PR:PRO_000022756 , Pride:P0A9S3 , Protein Model Portal:P0A9S3 , RefSeq:NP_416594 , RegulonDB:EG12417 , SMR:P0A9S3 , String:511145.b2091 , UniProt:P0A9S3

Relationship Links: InterPro:IN-FAMILY:IPR002085 , InterPro:IN-FAMILY:IPR002328 , InterPro:IN-FAMILY:IPR011032 , InterPro:IN-FAMILY:IPR013149 , InterPro:IN-FAMILY:IPR013154 , InterPro:IN-FAMILY:IPR016040 , Panther:IN-FAMILY:PTHR11695 , PDB:Structure:4A2C , Pfam:IN-FAMILY:PF00107 , Pfam:IN-FAMILY:PF08240 , Prosite:IN-FAMILY:PS00059

In Paralogous Gene Group: 103 (13 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019404 - galactitol catabolic process Inferred from experiment [Lengeler77]
GO:0019402 - galactitol metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred from experiment [Lengeler77]
GO:0042802 - identical protein binding Inferred from experiment [EstebanTorres12]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA01]
GO:0008868 - galactitol-1-phosphate 5-dehydrogenase activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for gatD 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]
Yes [Feist07, Comment 3]

Credits:
Last-Curated ? 06-Dec-2006 by Keseler I , SRI International


Enzymatic reaction of: galactitol-1-phosphate dehydrogenase

EC Number: 1.1.1.-

galactitol 1-phosphate + NAD+ <=> D-tagatofuranose 6-phosphate + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

In Pathways: superpathway of hexitol degradation (bacteria) , galactitol degradation

Kinetic Parameters:

Substrate
Km (μM)
Citations
galactitol 1-phosphate
300.0
[Lengeler77]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 38
[UniProt10a]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 59
[UniProt10a]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 89
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 92
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 95
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 103
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 144
[UniProt10a]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 213
[Nobelmann95, UniProt10]
Alternate sequence: S → L; UniProt: (in Ref. 1; CAA56231);
Sequence-Conflict 222
[Nobelmann95, UniProt10]
Alternate sequence: S → G; UniProt: (in Ref. 1; CAA56231);
Sequence-Conflict 226 -> 227
[Nobelmann95, UniProt10]
Alternate sequence: EL → DV; UniProt: (in Ref. 1; CAA56231);
Sequence-Conflict 271
[Nobelmann95, UniProt10]
Alternate sequence: A → T; UniProt: (in Ref. 1; CAA56231);
Sequence-Conflict 327 -> 329
[Nobelmann95, UniProt10]
Alternate sequence: AQA → TQV; UniProt: (in Ref. 1; CAA56231);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2091 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12417; 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

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

EstebanTorres12: Esteban-Torres M, Alvarez Y, Acebron I, de las Rivas B, Munoz R, Kohring GW, Roa AM, Sobrino M, Mancheno JM (2012). "The crystal structure of galactitol-1-phosphate 5-dehydrogenase from Escherichia coli K12 provides insights into its anomalous behavior on IMAC processes." FEBS Lett 586(19);3127-33. PMID: 22979983

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

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.

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

Lengeler75: Lengeler J (1975). "Nature and properties of hexitol transport systems in Escherichia coli." J Bacteriol 124(1);39-47. PMID: 1100608

Lengeler77: Lengeler J (1977). "Analysis of mutations affecting the dissmilation of galactitol (dulcitol) in Escherichia coli K 12." Mol Gen Genet 1977;152(1);83-91. PMID: 325390

Nobelmann95: Nobelmann B, Lengeler JW (1995). "Sequence of the gat operon for galactitol utilization from a wild-type strain EC3132 of Escherichia coli." Biochim Biophys Acta 1995;1262(1);69-72. PMID: 7772602

Nobelmann96: Nobelmann B, Lengeler JW (1996). "Molecular analysis of the gat genes from Escherichia coli and of their roles in galactitol transport and metabolism." J Bacteriol 1996;178(23);6790-5. PMID: 8955298

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Hollands07: Hollands K, Busby SJ, Lloyd GS (2007). "New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome." FEMS Microbiol Lett 274(1);89-94. PMID: 17608696

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

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470


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 Sun Dec 21, 2014, BIOCYC13A.