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
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
12/28 - 12/31
for maintenance.
twitter

MetaCyc Enzyme: diacylglycerol kinase

Gene: dgkA Accession Numbers: EG10224 (MetaCyc), b4042, ECK4034

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of diacylglycerol kinase = [DgkA]3

Summary:
Diacylglycerol kinase is the smallest known kinase. It functions in the recycling of diacylglycerol which is produced as a by-product of Membrane Derived Oligosaccharides (MDO) biosynthesis. Diacylglycerol is phosphorylated yielding phosphatidic acid, however the enzyme represents only a minor route in phosphatidic acid biosynthesis. In addition to the MgATP substrate, the enzyme requires a second divalent metal cation and a lipid cofactor for activity. The lipid cofactor induces a conformational change in the enzyme, switching it from a catalytically inactive form susceptible to inactivation to a catalytically active form resistant to inactivation [Russ88, Loomis85, Walsh86, Walsh90, Walsh92, Smith94].

The nuclear magnetic resonance (NMR) solution structure of the DgkA homotrimer has been reported [Van09] and regions of the protein important for folding and catalysis have been identified [Lau99, Van09].

The rate and yield of diacylglycerol kinase folding are increased by increasing the amount of phosphatidylglycerol (PG) in lipid vesicles [Seddon08].

Citations: [Savage07]

Locations: inner membrane

Map Position: [4,254,660 -> 4,255,028]

Molecular Weight of Polypeptide: 13.245 kD (from nucleotide sequence)

pI: 6.46

Unification Links: ASAP:ABE-0013235 , CGSC:862 , DIP:DIP-60228N , EchoBASE:EB0220 , EcoGene:EG10224 , EcoliWiki:b4042 , OU-Microarray:b4042 , PortEco:dgkA , PR:PRO_000022432 , Pride:P0ABN1 , Protein Model Portal:P0ABN1 , RefSeq:NP_418466 , RegulonDB:EG10224 , SMR:P0ABN1 , String:511145.b4042 , UniProt:P0ABN1

Relationship Links: InterPro:IN-FAMILY:IPR000829 , PDB:Structure:2KDC , PDB:Structure:3ZE3 , PDB:Structure:3ZE4 , PDB:Structure:3ZE5 , Pfam:IN-FAMILY:PF01219 , Prosite:IN-FAMILY:PS01069

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006654 - phosphatidic acid biosynthetic process Inferred from experiment [Russ88]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0008654 - phospholipid biosynthetic process Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004143 - diacylglycerol kinase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Russ88]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07, Daley05]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Loomis85]
GO:0016021 - integral component of membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, Smith94]

MultiFun Terms: cell structure membrane
metabolism biosynthesis of building blocks fatty acids and phosphatidic acid
metabolism biosynthesis of macromolecules (cellular constituents) phospholipid

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: diacylglycerol kinase

Synonyms: DAGK, diglyceride kinase, DGK, ATP:1,2-diacylglycerol 3-phosphotransferase

EC Number: 2.7.1.107

ATP + a 1,2-diacyl-sn-glycerol <=> a 1,2-diacyl-sn-glycerol 3-phosphate + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates [Comment 1]:

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:

Cofactors or Prosthetic Groups: Cd2+ , Zn2+ , Mg2+ , Mn2+ , Co2+

Inhibitors (Unknown Mechanism): 1,3-dioctanoylglycerol , 1,3-dioctanoyl-1,2,3-butanetriol , 1,2-dioctanoyl-3-methyl-1,2,3-butanetriol , 1,2-dioctanoyl-1,2,6-hexanetriol , 1,2-dioctanoyl-1,2,3-butanetriol , 1-monopalmitoylethylene glycol , 2-oleoylglycerol , 1,2-di-S-octyl-1,2-dimercapto-3-propanol , 1,2-di-O-octylglycerol , 2,3-dioctanoylglyceramide , 1,2-dioctanoyl-1-amino-2,3-propanediol , sn-1,2-di(2-propylpentanoyl)glycerol , 1,2-dioctanoyl-1,2,4-butanetriol , a 1,2-diacyl-sn-glycerol , Ca2+ [Walsh92]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
340.0
[Jittikoon07, BRENDA14]
ATP
1400.0
[Bohnenberger79, BRENDA14]

pH(opt): 6.3 [BRENDA14, Bohnenberger79]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Loomis85, UniProt11]
UniProt: Removed.
Chain 2 -> 122
[UniProt09]
UniProt: Diacylglycerol kinase;
Transmembrane-Region 34 -> 49
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probably;
Transmembrane-Region 53 -> 69
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probably;
Transmembrane-Region 96 -> 119
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probably;

History:
10/20/97 Gene b4042 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10224; confirmed by SwissProt match.


References

Bohnenberger79: Bohnenberger E, Sandermann H (1979). "Diglyceride kinase from Escherichia coli. Purification in organic solvent and some properties of the enzyme." Eur J Biochem 94(2);401-7. PMID: 218816

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

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.

Jittikoon07: Jittikoon J, East JM, Lee AG (2007). "A fluorescence method to define transmembrane alpha-helices in membrane proteins: studies with bacterial diacylglycerol kinase." Biochemistry 46(38);10950-9. PMID: 17722884

Lau99: Lau FW, Chen X, Bowie JU (1999). "Active sites of diacylglycerol kinase from Escherichia coli are shared between subunits." Biochemistry 1999;38(17);5521-7. PMID: 10220339

Loomis85: Loomis CR, Walsh JP, Bell RM (1985). "sn-1,2-Diacylglycerol kinase of Escherichia coli. Purification, reconstitution, and partial amino- and carboxyl-terminal analysis." J Biol Chem 1985;260(7);4091-7. PMID: 2984194

Russ88: Russ E, Kaiser U, Sandermann H (1988). "Lipid-dependent membrane enzymes. Purification to homogeneity and further characterization of diacylglycerol kinase from Escherichia coli." Eur J Biochem 1988;171(1-2);335-42. PMID: 2828054

Savage07: Savage DF, Anderson CL, Robles-Colmenares Y, Newby ZE, Stroud RM (2007). "Cell-free complements in vivo expression of the E. coli membrane proteome." Protein Sci 16(5);966-76. PMID: 17456747

Seddon08: Seddon AM, Lorch M, Ces O, Templer RH, Macrae F, Booth PJ (2008). "Phosphatidylglycerol lipids enhance folding of an alpha helical membrane protein." J Mol Biol 380(3);548-56. PMID: 18565344

Smith94: Smith RL, O'Toole JF, Maguire ME, Sanders CR (1994). "Membrane topology of Escherichia coli diacylglycerol kinase." J Bacteriol 1994;176(17);5459-65. PMID: 8071224

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

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

Van09: Van Horn WD, Kim HJ, Ellis CD, Hadziselimovic A, Sulistijo ES, Karra MD, Tian C, Sonnichsen FD, Sanders CR (2009). "Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase." Science 324(5935);1726-9. PMID: 19556511

Walsh86: Walsh JP, Bell RM (1986). "sn-1,2-Diacylglycerol kinase of Escherichia coli. Structural and kinetic analysis of the lipid cofactor dependence." J Biol Chem 1986;261(32);15062-9. PMID: 3021764

Walsh90: Walsh JP, Fahrner L, Bell RM (1990). "sn-1,2-diacylglycerol kinase of Escherichia coli. Diacylglycerol analogues define specificity and mechanism." J Biol Chem 1990;265(8);4374-81. PMID: 2155227

Walsh92: Walsh JP, Bell RM (1992). "Diacylglycerol kinase from Escherichia coli." Methods Enzymol 1992;209;153-62. PMID: 1323028

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, biocyc11.