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

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 [Reizer96c].

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) [Reizer96c, 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

Reizer96c: 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 Mon Dec 22, 2014, biocyc13.