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Escherichia coli K-12 substr. MG1655 Enzyme: lipopolysaccharide core heptose (II) kinase



Gene: waaY Accession Numbers: EG11425 (EcoCyc), b3625, ECK3615

Synonyms: rfaY

Regulation Summary Diagram: ?

Summary:
The lipopolysaccharide of E. coli K-12 consists of two major components: the hydrophobic lipid A moiety inserted into the outer membrane and the phosphorylated core oligosaccharide [Raetz02]. E. coli K-12 does not produce O antigen to attach to the LPS core due to a defect in the rfb gene cluster which can be complemented with genes from a second, independent rfb mutant to produce an O16 type O antigen [Stevenson94]. E. coli K-12 may have two major pathways for LPS biosynthesis. One generates LPS cores suitable for O antigen attachment, and a second generates lipooligosaccharides (LOS) with modifications to the core structure which prevent O antigen attachment [Klena92].

WaaY is a kinase responsible for phosphorylation of the heptose II residue in the inner core of LPS [Yethon98, Heinrichs98]. WaaY requires an intact waaG and waaP in order to phosphorylate the HepII residue in E. coli strain F470 [Yethon98, Yethon00].

Reviews: [Raetz02, Heinrichs98, Schnaitman93]
The chromosomal waa region (formerly rfa) contains the major core-oligosaccharide assembly operons in E. coli [Raetz02][Raetz07]. The current nomenclature system was proposed originally in [Reeves96] and [Heinrichs98] and followed thereafter.

Gene Citations: [Lee09e, Parker92, Klena92a]

Locations: cytosol, inner membrane

Map Position: [3,798,290 <- 3,798,988] (81.87 centisomes)
Length: 699 bp / 232 aa

Molecular Weight of Polypeptide: 27.461 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011856 , CGSC:33828 , EchoBASE:EB1395 , EcoGene:EG11425 , EcoliWiki:b3625 , Entrez-gene:948145 , OU-Microarray:b3625 , PortEco:rfaY , PR:PRO_000023727 , Pride:P27240 , Protein Model Portal:P27240 , RefSeq:NP_418082 , RegulonDB:EG11425 , SMR:P27240 , String:511145.b3625 , UniProt:P27240

Relationship Links: InterPro:IN-FAMILY:IPR009330 , InterPro:IN-FAMILY:IPR011009 , Pfam:IN-FAMILY:PF06176

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0016310 - phosphorylation Inferred from experiment Inferred by computational analysis [UniProtGOA11, Yethon98]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009244 - lipopolysaccharide core region biosynthetic process Inferred by computational analysis [UniProtGOA12, GOA01]
Molecular Function: 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]
GO:0016772 - transferase activity, transferring phosphorus-containing groups Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005886 - plasma membrane

MultiFun Terms: cell structure surface antigens (ECA, O antigen of LPS)
metabolism biosynthesis of macromolecules (cellular constituents) lipopolysaccharide core region

Essentiality data for waaY 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:
Reviewed 22-Feb-2010 by Sarker M


Enzymatic reaction of: lipopolysaccharide core heptose (II) kinase

EC Number: 2.7.1.-

glucosyl-(heptosyl)3-Kdo2-lipid A-phosphate + ATP <=> glucosyl-(heptosyl)3-Kdo2-lipid A-bisphosphate + 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 favored in the direction shown.

In Pathways: superpathway of lipopolysaccharide biosynthesis , Lipid A-core biosynthesis


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 51 -> 52
[Klena92a, UniProt10a]
Alternate sequence: DT → VS; UniProt: (in Ref. 1; AAA24521);
Sequence-Conflict 145 -> 146
[Klena92a, UniProt10a]
Alternate sequence: QQ → HE; UniProt: (in Ref. 1; AAA24521);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3625 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11425; 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

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."

Heinrichs98: Heinrichs DE, Yethon JA, Whitfield C (1998). "Molecular basis for structural diversity in the core regions of the lipopolysaccharides of Escherichia coli and Salmonella enterica." Mol Microbiol 30(2);221-32. PMID: 9791168

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

Klena92: Klena JD, Ashford RS, Schnaitman CA (1992). "Role of Escherichia coli K-12 rfa genes and the rfp gene of Shigella dysenteriae 1 in generation of lipopolysaccharide core heterogeneity and attachment of O antigen." J Bacteriol 174(22);7297-307. PMID: 1385388

Klena92a: Klena JD, Pradel E, Schnaitman CA (1992). "Comparison of lipopolysaccharide biosynthesis genes rfaK, rfaL, rfaY, and rfaZ of Escherichia coli K-12 and Salmonella typhimurium." J Bacteriol 174(14);4746-52. PMID: 1624462

Lee09e: Lee JH, Lee KL, Yeo WS, Park SJ, Roe JH (2009). "SoxRS-mediated lipopolysaccharide modification enhances resistance against multiple drugs in Escherichia coli." J Bacteriol 191(13);4441-50. PMID: 19376854

Parker92: Parker CT, Kloser AW, Schnaitman CA, Stein MA, Gottesman S, Gibson BW (1992). "Role of the rfaG and rfaP genes in determining the lipopolysaccharide core structure and cell surface properties of Escherichia coli K-12." J Bacteriol 174(8);2525-38. PMID: 1348243

Raetz02: Raetz CR, Whitfield C (2002). "Lipopolysaccharide endotoxins." Annu Rev Biochem 71;635-700. PMID: 12045108

Raetz07: Raetz CR, Reynolds CM, Trent MS, Bishop RE (2007). "Lipid A modification systems in gram-negative bacteria." Annu Rev Biochem 76;295-329. PMID: 17362200

Reeves96: Reeves PR, Hobbs M, Valvano MA, Skurnik M, Whitfield C, Coplin D, Kido N, Klena J, Maskell D, Raetz CR, Rick PD (1996). "Bacterial polysaccharide synthesis and gene nomenclature." Trends Microbiol 4(12);495-503. PMID: 9004408

Schnaitman93: Schnaitman CA, Klena JD (1993). "Genetics of lipopolysaccharide biosynthesis in enteric bacteria." Microbiol Rev 57(3);655-82. PMID: 7504166

Stevenson94: Stevenson G, Neal B, Liu D, Hobbs M, Packer NH, Batley M, Redmond JW, Lindquist L, Reeves P (1994). "Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster." J Bacteriol 1994;176(13);4144-56. PMID: 7517391

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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Yethon00: Yethon JA, Vinogradov E, Perry MB, Whitfield C (2000). "Mutation of the lipopolysaccharide core glycosyltransferase encoded by waaG destabilizes the outer membrane of Escherichia coli by interfering with core phosphorylation." J Bacteriol 182(19);5620-3. PMID: 10986272

Yethon98: Yethon JA, Heinrichs DE, Monteiro MA, Perry MB, Whitfield C (1998). "Involvement of waaY, waaQ, and waaP in the modification of Escherichia coli lipopolysaccharide and their role in the formation of a stable outer membrane." J Biol Chem 273(41);26310-6. PMID: 9756860

Other References Related to Gene Regulation

Clementz92: Clementz T (1992). "The gene coding for 3-deoxy-manno-octulosonic acid transferase and the rfaQ gene are transcribed from divergently arranged promoters in Escherichia coli." J Bacteriol 1992;174(23);7750-6. PMID: 1447141

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637


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 Thu Nov 27, 2014, BIOCYC13B.