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



Gene: yegS Accession Numbers: G7123 (EcoCyc), b2086, ECK2082

Regulation Summary Diagram: ?

Summary:
YegS is a lipid kinase with phosphatidylglycerol kinase activity in vitro [Bakali07]. It shows sequence similarity to a family of eukaryotic non-protein kinases [Bakali06]. The physiological role of YegS is unknown, but a possible role in the response to acid stress has been proposed [Bakali07].

A crystal structure of YegS has been determined at 1.9 Å resolution; the protein shows structural similarity to a family of NAD kinases [Bakali06, Bakali07].

Locations: cytosol

Map Position: [2,166,736 -> 2,167,635] (46.7 centisomes)
Length: 900 bp / 299 aa

Molecular Weight of Polypeptide: 32.039 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006911 , DIP:DIP-11889N , EchoBASE:EB4111 , EcoGene:EG14367 , EcoliWiki:b2086 , OU-Microarray:b2086 , PortEco:yegS , Pride:P76407 , Protein Model Portal:P76407 , RefSeq:NP_416590 , RegulonDB:G7123 , SMR:P76407 , String:511145.b2086 , UniProt:P76407

Relationship Links: InterPro:IN-FAMILY:IPR001206 , InterPro:IN-FAMILY:IPR005218 , InterPro:IN-FAMILY:IPR016064 , InterPro:IN-FAMILY:IPR022433 , InterPro:IN-FAMILY:IPR022862 , PDB:Structure:2BON , PDB:Structure:2JGR , Pfam:IN-FAMILY:PF00781 , Prosite:IN-FAMILY:PS50146 , Smart:IN-FAMILY:SM00046

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0046834 - lipid phosphorylation Inferred by computational analysis Inferred from experiment [Bakali07, GOA06, GOA01a]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0007205 - protein kinase C-activating G-protein coupled receptor signaling pathway Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0008654 - phospholipid biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0001727 - lipid kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Bakali07]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003951 - NAD+ kinase activity Inferred by computational analysis [GOA01a]
GO:0004143 - diacylglycerol kinase activity Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol [Bakali07]

MultiFun Terms: metabolism

Essentiality data for yegS 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 ? 26-Mar-2007 by Keseler I , SRI International


Enzymatic reaction of: lipid kinase

Synonyms: phosphatidylglycerol kinase

an L-1-phosphatidyl-glycerol + ATP <=> an L-1-phosphatidylglycerol-phosphate + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Summary:
Enzymatic activity is absolutely dependent on the presence of a metal ion (Ca2+ or Mg2+); the activity profile with these two metal ions is complex [Bakali07].

Cofactors or Prosthetic Groups: Ca2+ [Bakali07]

Kinetic Parameters:

Substrate
Km (μM)
Citations
an L-1-phosphatidyl-glycerol
700.0
[Bakali07]

pH(opt): 7.5 [Bakali07]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 2 -> 133
[UniProt09]
UniProt: DAGKc;
Amino-Acid-Sites-That-Bind 40
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 66 -> 72
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 95
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 215
[UniProt10a]
UniProt: Magnesium; via carbonyl oxygen;
Metal-Binding-Site 218
[UniProt10a]
UniProt: Magnesium;
Metal-Binding-Site 220
[UniProt10a]
UniProt: Magnesium; via carbonyl oxygen;
Active-Site 271
[UniProt10]
UniProt: Proton acceptor; 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

Bakali06: Bakali MA, Nordlund P, Hallberg BM (2006). "Expression, purification, crystallization and preliminary diffraction studies of the mammalian DAG kinase homologue YegS from Escherichia coli." Acta Crystallograph Sect F Struct Biol Cryst Commun 62(Pt 3);295-7. PMID: 16511327

Bakali07: Bakali MA, Dolores Herman M, Johnson KA, Kelly A, Wieslander A, Hallberg BM, Nordlund P (2007). "Crystal structure of YegS a homologue to the mammalian diacylglycerol kinases, reveals a novel regulatory metal binding site." J Biol Chem 282(27):19644-52. PMID: 17351295

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

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


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 Nov 23, 2014, BIOCYC13A.