Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: N-acetyl-D-galactosamine PTS permease (cryptic) - AgaW subunit (pseudogene)



Gene: agaW Accession Numbers: G7633 (EcoCyc), b3134, ECK3122

Synonyms: yhaZ, EIIC'Aga, EIIC'GalNAc, Enzyme IIC'Aga, Enzyme IIC'GalNAc

Regulation Summary Diagram: ?

Component of: N-acetyl-D-galactosamine PTS permease (cryptic) (extended summary available)

Summary:
Sequence analysis predicts that agaW encodes a truncated protein with similarity to the N-terminal region of the of IIC proteins of the PTS Enzymes II specific for mannose [Reizer96].

E. coli K-12 does not contain the genes encoding Enzymes IIDAga and IIAAga (encoded by agaE and agaF in E. coli strains B and C). In addition the agaW gene, encoding an Enzyme IICAga and agaA encoding a deacetylase have been truncated and thus K-12 is unable to use D-galactosamine (GalN) or N-acetyl-D-galactosamine (GalNAc) as a carbon source [Brinkkotter00].

Locations: inner membrane

Map Position: [3,278,723 -> 3,279,124] (70.67 centisomes)
Length: 402 bp / 133 aa

Molecular Weight of Polypeptide: 13.721 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010299 , EchoBASE:EB2618 , EcoGene:EG12765 , EcoliWiki:b3134 , OU-Microarray:b3134 , PortEco:agaW , Protein Model Portal:P42905 , RefSeq:NP_417603 , RegulonDB:G7633 , UniProt:P42905

Relationship Links: EcoO157Cyc:Homolog:Z4486 , EcoO157Cyc:Homolog:Z4486-MONOMER , InterPro:IN-FAMILY:IPR004700 , Pfam:IN-FAMILY:PF03609 , Prosite:IN-FAMILY:PS51106

In Paralogous Gene Group: 495 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0008643 - carbohydrate transport Inferred by computational analysis [UniProtGOA11]
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: All-Genes Pseudo-Genes
MultiFun transport Group Translocators Phosphotransferase Systems (PEP-dependent PTS)

Essentiality data for agaW 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]

Subunit of: N-acetyl-D-galactosamine PTS permease (cryptic)

Subunit composition of N-acetyl-D-galactosamine PTS permease (cryptic) = [AgaV][AgaW]
         N-acetyl-D-galactosamine PTS permease (cryptic) - AgaV subunit = AgaV (summary available)
         N-acetyl-D-galactosamine PTS permease (cryptic) - AgaW subunit (pseudogene) = AgaW (summary available)

Summary:
E. coli contains a cluster of genes (agaZVWEFASYBCDI) responsible for the uptake and metabolism of D-galactosamine (GalN or Gam) and N-acetyl-D-galactosamine (GalNAc or Aga). However, in strain K-12 there is a deletion of the region from agaW' to 'agaA making this organism unable to utilize GalN and GalNAc as sole carbon sources [Brinkkotter00].

AgaVWEF, the cryptic GalNAc PTS permease, belongs to the functional superfamily of the PEP-dependent, sugar transporting phosphotransferase system (PTSsugar). If all of its components were present, AgaVWEF would take up exogenous GalNAc, releasing the phosphate ester into the cell cytoplasm in preparation for metabolism [Postma93, Brinkkotter00].

AgaV is an Enzyme IIBAga. AgaW is a truncated Enzyme IICAga. agaE and agaF encoding Enzymes IIDAga and IIAAga/Gam, respectively, have been deleted. All of these proteins are homologous to the mannose Enzyme II complex proteins (the splinter group enzymes) [Reizer96, Brinkkotter00].

The aga operon (agaZVW' 'ASYBCDI) also encodes other enzymes for the metabolism of GalNAc and GalN: GalNAc-6-phosphate deacetylase (AgaA), a putative isomerase (AgaS), a tagatose-bisphosphate aldolase (AgaYZ) and a GalN-6-phosphate deaminase (AgaI). The truncated agaA gene in E. coli K-12 is inactive. The agaR gene, encoding a transcriptional repressor of the aga operon, precedes and is divergently transcribed from the aga operon [Brinkkotter00, Ray04]

Credits:
Created 26-Jun-2007 by Johnson A , TIGR
Last-Curated ? 05-May-2014 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 133
[UniProt09]
UniProt: PTS EIIC type-4;
Transmembrane-Region 3 -> 23
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 33 -> 53
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 66 -> 86
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 94 -> 114
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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

Brinkkotter00: Brinkkotter A, Kloss H, Alpert C, Lengeler JW (2000). "Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli." Mol Microbiol 2000;37(1);125-35. PMID: 10931310

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Postma93: Postma PW, Lengeler JW, Jacobson GR (1993). "Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria." Microbiol Rev 57(3);543-94. PMID: 8246840

Ray04: Ray WK, Larson TJ (2004). "Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12." Mol Microbiol 51(3);813-26. PMID: 14731281

Reizer96: Reizer J, Ramseier TM, Reizer A, Charbit A, Saier MH (1996). "Novel phosphotransferase genes revealed by bacterial genome sequencing: a gene cluster encoding a putative N-acetylgalactosamine metabolic pathway in Escherichia coli." Microbiology 1996;142 ( Pt 2);231-50. PMID: 8932697

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.

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."


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 Sat Nov 22, 2014, BIOCYC14A.