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Escherichia coli K-12 substr. MG1655 Enzyme: dihydroxyacetone kinase

Synonyms: DHAK


Subunit composition of dihydroxyacetone kinase = [DhaM]2[DhaK]2[DhaL]
         dihydroxyacetone kinase subunit M = DhaM (summary available)
         dihydroxyacetone kinase subunit K = DhaK (summary available)
         dihydroxyacetone kinase subunit L = DhaL (summary available)

Summary:
Dihydroxyacetone (DHA) can serve as the sole source of carbon and energy for E. coli K-12 but only in a low phosphate environment (possibly due to the build up of methylglyoxal [Jin84].

Dihydroxyacetone kinase, which is composed of the three subunits DhaK, DhaL, and DhaM, functions similarly to a phosphotransferase system (PTS) in that it utilizes phosphoenolpyruvate as a phosphoryl donor. It differs in not being involved in transport. The phosphorylation reaction requires the presence of the EI and HPr proteins of the PTS system. The DhaM subunit is phosphorylated at multiple sites [Gutknecht01]. DhaK contains the substrate binding site [Siebold03, GarciaAlles04].

The DhaK and DhaL subunits act antagonistically as corepressor and coactivator of the DhaR transcription factor that controls expression of the dhaKLM operon [Bachler05].

Other dihydroxyacetone kinases found in other bacteria, animals, and plants utilize ATP. Two of the subunits, DhaK and DhaL, are homologous to the ATP-dependent dihydroxyacetone kinases. Another subunit, DhaM is homologous to certain components of PTS: to a domain of EI, to HPr, and to the AB domains of EII.

The product of this reaction, dihydroxyacetone phosphate, is also formed by a flavin-dependent oxidation of glycerol-3-phosphate. Dihydroxyacetone phosphate is further metabolized through the glycolytic pathway.

A mutant lacking EI can not phosphorylate DHA [Jin84].

Review: [Erni06]

Locations: cytosol

Molecular Weight: 204.8 kD (experimental) [Gutknecht01]

Gene-Reaction Schematic

Gene-Reaction Schematic


GO Terms:
Cellular Component:
GO:0005829 - cytosol [Gutknecht01]

Enzymatic reaction of: dihydroxyacetone kinase

Inferred from experiment

EC Number: 2.7.1.121

dihydroxyacetone + phosphoenolpyruvate → glycerone phosphate + pyruvate

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: glycerol degradation V

Summary:
Kd, Km and Kcat values for a variety of substrates have been measured [GarciaAlles04].

Kinetic Parameters:
Substrate Km (μM) Citations
dihydroxyacetone 6.0 [GarciaAlles04]

Subunit of dihydroxyacetone kinase: dihydroxyacetone kinase subunit M

Synonyms: DhaM, DhaH, YcgC, PtsD

Gene: dhaM Accession Numbers: EG12399 (EcoCyc), b1198, ECK1186

Locations: cytosol, membrane

Sequence Length: 472 AAs

Molecular Weight: 51.449 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred from experimentGO:0006974 - cellular response to DNA damage stimulus [Khil02]
Inferred by computational analysisGO:0006071 - glycerol metabolic process [UniProtGOA11a]
Inferred by computational analysisGO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016310 - phosphorylation [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0019563 - glycerol catabolic process [UniProtGOA12]
Molecular Function:
Inferred from experimentGO:0042803 - protein homodimerization activity [Gutknecht01]
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a]
Inferred by computational analysisGO:0016301 - kinase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016772 - transferase activity, transferring phosphorus-containing groups [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]
Inferred by computational analysisGO:0016021 - integral component of membrane [GOA01a]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds

Unification Links: DIP:DIP-11551N, EcoliWiki:b1198, ModBase:P37349, PR:PRO_000022440, Pride:P37349, Protein Model Portal:P37349, RefSeq:NP_415716, SMR:P37349, UniProt:P37349

Relationship Links: InterPro:IN-FAMILY:IPR000032, InterPro:IN-FAMILY:IPR001020, InterPro:IN-FAMILY:IPR004701, InterPro:IN-FAMILY:IPR008279, InterPro:IN-FAMILY:IPR008731, InterPro:IN-FAMILY:IPR012844, Pfam:IN-FAMILY:PF00381, Pfam:IN-FAMILY:PF00391, Pfam:IN-FAMILY:PF03610, Pfam:IN-FAMILY:PF05524, Prints:IN-FAMILY:PR00107, Prosite:IN-FAMILY:PS00369, Prosite:IN-FAMILY:PS51096, Prosite:IN-FAMILY:PS51350

Summary:
The M subunit is homologous to certain components of PTS: to a domain of EI, to HPr, and to the AB domains of EII. DhaM can be phosphorylated in vitro by phosphoenolpyruvate in the presence of EI and HPr and serves as the phosphoryl donor of the dihydroxyacetone kinase reaction [Paulsen00, Gutknecht01].

DhaM forms a homodimer in solution [Gutknecht01].

DhaM: "dihydroxyacetone" [Gutknecht01]

Essentiality data for dhaM knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of dihydroxyacetone kinase: dihydroxyacetone kinase subunit K

Synonyms: YcgT, DhaK

Gene: dhaK Accession Numbers: G6627 (EcoCyc), b1200, ECK1188

Locations: cytosol

Sequence Length: 356 AAs

Molecular Weight: 38.215 kD (from nucleotide sequence)

Molecular Weight: 40.0 kD (experimental) [Paulsen00]


GO Terms:
Biological Process:
Inferred from experimentGO:0006974 - cellular response to DNA damage stimulus [Khil02]
Inferred from experimentGO:0042182 - ketone catabolic process [Paulsen00]
Inferred from experimentGO:0046365 - monosaccharide catabolic process [Paulsen00]
Inferred by computational analysisGO:0006071 - glycerol metabolic process [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016310 - phosphorylation [UniProtGOA11a]
Inferred by computational analysisGO:0019563 - glycerol catabolic process [UniProtGOA12]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Bachler05]
Inferred from experimentGO:0047324 - phosphoenolpyruvate-glycerone phosphotransferase activity [Paulsen00]
Inferred by computational analysisGO:0004371 - glycerone kinase activity [GOA01a]
Inferred by computational analysisGO:0016301 - kinase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, Lasserre06]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds

Unification Links: DIP:DIP-11563N, EcoliWiki:b1200, ModBase:P76015, PR:PRO_000022438, Pride:P76015, Protein Model Portal:P76015, RefSeq:NP_415718, SMR:P76015, UniProt:P76015

Relationship Links: InterPro:IN-FAMILY:IPR004006, InterPro:IN-FAMILY:IPR012736, PDB:Structure:1OI2, PDB:Structure:1OI3, PDB:Structure:1UOD, PDB:Structure:1UOE, PDB:Structure:3PNK, PDB:Structure:3PNL, PDB:Structure:3PNM, PDB:Structure:3PNO, PDB:Structure:3PNQ, PDB:Structure:4LRX, PDB:Structure:4LRY, Pfam:IN-FAMILY:PF02733, Prosite:IN-FAMILY:PS51481

Summary:
The K subunit is similar to the N-terminal half of ATP-dependent dihydroxyacetone kinase of Citrobacter freundii and eukaryotes. It exists in holoenzyme as a homodimer, consisting of two six-stranded mixed beta-sheets surrounded by nine alpha-helices and a beta-ribbon.

Crystal structures of apo-DhaK and DhaK in complex with dihydroxyacetone [Siebold03] as well as glyceraldehyde or dihydroxyacetone-phosphate [GarciaAlles04] have been solved. DhaK is a homodimer in the crystal structure [Siebold03].

DhaK is a corepressor of DhaR, the transcription factor that controls expression of the dhaKLM operon [Bachler05].

The levels of DhaK and DhaL are increased in a ptsI mutant [Beutler01].

A dhaK transposon insertion mutant is defective for growth on and phosphorylation of dihydroxyacetone [Paulsen00].

DhaK: "dihydroxyacetone" [Gutknecht01]

Essentiality data for dhaK knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of dihydroxyacetone kinase: dihydroxyacetone kinase subunit L

Synonyms: YcgS, DhaL, YsgS

Gene: dhaL Accession Numbers: G6626 (EcoCyc), b1199, ECK1187

Locations: cytosol

Sequence Length: 210 AAs

Molecular Weight: 22.632 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006071 - glycerol metabolic process [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016310 - phosphorylation [UniProtGOA11a]
Inferred by computational analysisGO:0019563 - glycerol catabolic process [UniProtGOA12]
Molecular Function:
Inferred from experimentGO:0000287 - magnesium ion binding [Oberholzer06]
Inferred from experimentGO:0005515 - protein binding [Bachler05]
Inferred from experimentGO:0043531 - ADP binding [Bachler05a]
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a]
Inferred by computational analysisGO:0004371 - glycerone kinase activity [GOA01a]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a]
Inferred by computational analysisGO:0016301 - kinase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016772 - transferase activity, transferring phosphorus-containing groups [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds

Unification Links: DIP:DIP-11562N, EcoliWiki:b1199, ModBase:P76014, PR:PRO_000022439, Pride:P76014, Protein Model Portal:P76014, RefSeq:NP_415717, SMR:P76014, UniProt:P76014

Relationship Links: InterPro:IN-FAMILY:IPR004007, InterPro:IN-FAMILY:IPR012737, PDB:Structure:2BTD, PDB:Structure:3PNL, PDB:Structure:4LRZ, Pfam:IN-FAMILY:PF02734, Prosite:IN-FAMILY:PS51480

Summary:
The L subunit is similar to the C-terminal half of ATP-dependent dihydroxyacetone kinases of eukaryotes and other bacteria. DhaL contains bound ADP which is transiently phosphorylated as a cofactor in the kinase reaction [Bachler05a].

A crystal structure of the DhaL-ADP comples has been solved at 2.6 Å resolution [Oberholzer06].

ADP-bound DhaL is a coactivator of DhaR, the transcription factor that controls expression of the dhaKLM operon [Bachler05].

The levels of DhaK and DhaL are increased in a ptsI mutant [Beutler01].

DhaL: "dihydroxyacetone" [Gutknecht01]

Essentiality data for dhaL knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

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

Bachler05: Bachler C, Schneider P, Bahler P, Lustig A, Erni B (2005). "Escherichia coli dihydroxyacetone kinase controls gene expression by binding to transcription factor DhaR." EMBO J 24(2);283-93. PMID: 15616579

Bachler05a: Bachler C, Flukiger-Bruhwiler K, Schneider P, Bahler P, Erni B (2005). "From ATP as substrate to ADP as coenzyme: functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases." J Biol Chem 280(18);18321-5. PMID: 15753087

Beutler01: Beutler R, Kampfer U, Schaller J, Erni B (2001). "Heterodimeric dihydroxyacetone kinase from a ptsI mutant of Escherichia coli." Microbiology 147(Pt 2);249-50. PMID: 11158340

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

Erni06: Erni B, Siebold C, Christen S, Srinivas A, Oberholzer A, Baumann U (2006). "Small substrate, big surprise: fold, function and phylogeny of dihydroxyacetone kinases." Cell Mol Life Sci 63(7-8);890-900. PMID: 16505971

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

GarciaAlles04: Garcia-Alles LF, Siebold C, Nyffeler TL, Flukiger-Bruhwiler K, Schneider P, Burgi HB, Baumann U, Erni B (2004). "Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism." Biochemistry 43(41);13037-45. PMID: 15476397

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Gutknecht01: Gutknecht R, Beutler R, Garcia-Alles LF, Baumann U, Erni B (2001). "The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor." EMBO J 20(10);2480-6. PMID: 11350937

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

Jin84: Jin RZ, Lin EC (1984). "An inducible phosphoenolpyruvate: dihydroxyacetone phosphotransferase system in Escherichia coli." J Gen Microbiol 130(1);83-8. PMID: 6368745

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Oberholzer06: Oberholzer AE, Schneider P, Baumann U, Erni B (2006). "Crystal structure of the nucleotide-binding subunit DhaL of the Escherichia coli dihydroxyacetone kinase." J Mol Biol 359(3);539-45. PMID: 16647083

Paulsen00: Paulsen IT, Reizer J, Jin RZ, Lin EC, Saier MH (2000). "Functional genomic studies of dihydroxyacetone utilization in Escherichia coli." Microbiology 146 ( Pt 10);2343-4. PMID: 11021910

Siebold03: Siebold C, Garcia-Alles LF, Erni B, Baumann U (2003). "A mechanism of covalent substrate binding in the x-ray structure of subunit K of the Escherichia coli dihydroxyacetone kinase." Proc Natl Acad Sci U S A 100(14);8188-92. PMID: 12813127

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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