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: galactosamine PTS permease (cryptic) - AgaD subunit



Gene: agaD Accession Numbers: G7635 (EcoCyc), b3140, ECK3128

Synonyms: yraF

Regulation Summary Diagram: ?

Component of: galactosamine PTS permease (cryptic) (extended summary available)

Summary:
Sequence analysis indicates that agaD encodes a protein with similarity to the IID domain of the PTS Enzymes II specific for mannose. agaD encodes a protein with a hydrophilic N-termini and a hydrophobic central and C-terminal region containing of 4-6 transmembrane regions [Reizer96].

agaD encodes the Enzyme IID domain of a predicted galactosamine (Gam or GalN) transporting PEP-dependent phosphotransferase system. E. coli K-12 cannot transport galactosamine as it is lacking an Enzyme IIA domain for this PTS (encoded by the agaF gene in E. coli strains B and C). Providing agaF on a plasmid results in a Gam+ phenotype [Brinkkotter00].

Locations: inner membrane

Map Position: [3,283,500 -> 3,284,291] (70.77 centisomes)
Length: 792 bp / 263 aa

Molecular Weight of Polypeptide: 29.001 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010314 , EchoBASE:EB2624 , EcoGene:EG12771 , EcoliWiki:b3140 , OU-Microarray:b3140 , PortEco:agaD , PR:PRO_000022067 , Protein Model Portal:P42911 , RefSeq:NP_417609 , RegulonDB:G7635 , String:511145.b3140 , UniProt:P42911

Relationship Links: InterPro:IN-FAMILY:IPR004704 , InterPro:IN-FAMILY:IPR018405 , Pfam:IN-FAMILY:PF03613 , Prosite:IN-FAMILY:PS51108

In Paralogous Gene Group: 497 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a]
GO:0008643 - carbohydrate transport Inferred by computational analysis [UniProtGOA11a]
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

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

Essentiality data for agaD 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]

Subunit of: galactosamine PTS permease (cryptic)

Synonyms: EIIGam, Enzyme IIGam, EIIGalN, Enzyme IIGalN

Subunit composition of galactosamine PTS permease (cryptic) = [AgaB][AgaC][AgaD]
         galactosamine PTS permease (cryptic) - AgaB subunit = AgaB (summary available)
         galactosamine PTS permease (cryptic) - AgaC subunit = AgaC (summary available)
         galactosamine PTS permease (cryptic) - AgaD subunit = AgaD (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].

AgaBCD, the cryptic GalN PTS permease, belongs to the functional superfamily of the phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system (PTSsugar). The PTSsugar transports and simultaneously phosphorylates its substrates in a process called group translocation (reviewed in [Postma93]). When all of its components are present, AgaBCDF takes up exogenous GalN, releasing the phosphate ester into the cell cytoplasm in preparation for metabolism [Brinkkotter00].

AgaB is Enzymes IIBGam. AgaC is Enzyme IICGam. AgaD is an Enzyme IIDGam. agaF encoding Enzyme IIAAga/Gam has been deleted. All of these proteins are homologous to the mannose Enzyme II complex proteins (the splinter group enzymes) [Reizer96, Brinkkotter00].

E. coli K-12 is Gam- Aga-. Providing agaF (which encodes a PTS Enzyme IIA domain) from E. coli C on a plasmid results in a Gam+ Aga- phenotype [Brinkkotter00].

The aga gene cluster (agaZVWASYBCDI) also encodes other enzymes for the metabolism of GalNAc and GalN: GalNAc-6-phosphate deacetylase (AgaA), a putative isomerase (AgaS), a tagatose-bisphosphate aldolase (KbaYZ formerly AgaYZ) and a GalN-6-phosphate deaminase (AgaI). The truncated agaA gene in E. coli K-12 is inactive. agaR encodes a transcriptional repressor of the aga gene cluster [Brinkkotter00, Ray04].

Credits:
Last-Curated ? 01-May-2014 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 3 -> 263
[UniProt09]
UniProt: PTS EIID;
Transmembrane-Region 61 -> 81
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 98 -> 118
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 131 -> 151
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 178 -> 198
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 215 -> 235
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 243 -> 263
[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

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

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."

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 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 Sat Nov 22, 2014, BIOCYC13A.