Escherichia coli K-12 substr. MG1655 Polypeptide: dihydroxyacetone kinase subunit M

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

Synonyms: ycgC, dhaH, ptsD

Regulation Summary Diagram

Regulation summary diagram for dhaM

Component of: dihydroxyacetone kinase (extended summary available)

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]

Gene Citations: [Bachler05]

Locations: cytosol, membrane

Map Position: [1,246,919 <- 1,248,337] (26.88 centisomes, 97°)
Length: 1419 bp / 472 aa

Molecular Weight of Polypeptide: 51.449 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004024, DIP:DIP-11551N, EchoBASE:EB2299, EcoGene:EG12399, EcoliWiki:b1198, ModBase:P37349, OU-Microarray:b1198, PortEco:dhaM, PR:PRO_000022440, Pride:P37349, Protein Model Portal:P37349, RefSeq:NP_415716, RegulonDB:EG12399, SMR:P37349, String:511145.b1198, 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

In Paralogous Gene Group: 259 (4 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for dhaM

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

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

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)

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]

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

Enzymatic reaction of: dihydroxyacetone kinase

Inferred from experiment

EC Number:

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

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

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

Sequence Features

Protein sequence of dihydroxyacetone kinase subunit M with features indicated

Feature Class Location Citations Comment
Conserved-Region 1 -> 135
Inferred by computational analysis[UniProt15]
UniProt: PTS EIIA type-4.
Mutagenesis-Variant 9
Inferred from experiment[Gutknecht01]
UniProt: Loss of activity.
Active-Site 9
Author statement[UniProt15]
UniProt: Tele-phosphohistidine intermediate; for EIIA activity.
Conserved-Region 155 -> 242
Inferred by computational analysis[UniProt15]
UniProt: HPr.
Mutagenesis-Variant 169
Inferred from experiment[Gutknecht01]
UniProt: Loss of activity.
Active-Site 169
Author statement[UniProt15]
UniProt: Pros-phosphohistidine intermediate; for HPr activity.
Protein-Segment 264 -> 472
Author statement[UniProt15]
UniProt: PTS EI; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 430
Inferred from experiment[Gutknecht01]
UniProt: Loss of activity.
Active-Site 430
Inferred by curator[UniProt15]
UniProt: Tele-phosphohistidine intermediate.

Sequence Pfam Features

Protein sequence of dihydroxyacetone kinase subunit M with features indicated

Feature Class Location Citations Comment
Pfam PF03610 4 -> 120
Inferred by computational analysis[Finn14]
EIIA-man : PTS system fructose IIA component
Pfam PF00381 160 -> 236
Inferred by computational analysis[Finn14]
PTS-HPr : PTS HPr component phosphorylation site
Pfam PF05524 258 -> 368
Inferred by computational analysis[Finn14]
PEP-utilisers_N : PEP-utilising enzyme, N-terminal
Pfam PF00391 393 -> 464
Inferred by computational analysis[Finn14]
PEP-utilizers : PEP-utilising enzyme, mobile domain

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06].
10/20/97 Gene b1198 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12399; 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

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

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

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

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

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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."

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

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

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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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