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 Transporter: 4-aminobutyrate:H+ symporter



Gene: gabP Accession Numbers: EG11330 (EcoCyc), b2663, ECK2657

Synonyms: GabP APC transporter

Regulation Summary Diagram: ?

Summary:
GabP is a 4-aminobutyrate (GABA) transporter that is a member of the Amino Acid Polyamine Organocation (APC) Superfamily of transporters [Jack00]. Expression of the cloned gabP on a plasmid vector resulted in a 5-fold increase in GABA uptake. The apparent Km of GABA uptake was found to be 11.8 μM, and the Vmax was 0.33 nmol/min/g cells [Niegemann93].

Transport of GABA is dependent upon the presence of phosphatidylethanolamine (PE) within the membrane. In cells lacking PE, the N-terminal hairpin of GabP is inverted, and there is a hinge point in transmembrane domain III. Transport of GABA is reduced by over 99% under these conditions [Zhang05g]. The specificity of GabP has been investigated by measuring the effects of excess concentrations of various amino acids on the rate of radioactively labeled GABA uptake. Of the twenty protein amino acids, only aspartate could compete with GABA for uptake [Niegemann93]. Counterflow assays indicate that GabP is able to transport synthetic compounds with little structural resemblance to GABA, such as 3-piperidinecarboxylic acid and 3-hydroxy-5-aminomethylisoxazole, while other more structurally similar compounds such as 2-(aminomethyl)-5-hydroxy-4H-pyran-4-one and 4-amino-trans-butenoic acid, were not transported [Brechtel96]. The inhibitory action of the uncoupler 2, 4-dinitrophenol indicated the energy dependence of GABA uptake. Ammonium sulfate, known to increase membrane potential, stimulated GABA uptake significantly [Niegemann93]. Based on hydropathy analysis, LacZ, and PhoA fusions, GabP is believed to have 12 transmembrane segments [Hu98]. C300 of GabP appears to have a large functional significance, since replacing C300 with A, S, G, K, D, Y or P resulted in a marked loss in transport activity [Hu98a].

The gabT gene was identified in a search for mutants that have lost the ability to utilize 4-aminobutyrate (GABA) as a nitrogen source [Metzer79]. Regulation of the operon containing gabT has been studied extensively [Marschall98, Becker01a, Germer01, Metzner04].

Gene Citations: [Schneider02]

Locations: inner membrane

Map Position: [2,792,275 -> 2,793,675] (60.18 centisomes)
Length: 1401 bp / 466 aa

Molecular Weight of Polypeptide: 51.08 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008763 , CGSC:728 , DIP:DIP-9724N , EchoBASE:EB1306 , EcoGene:EG11330 , EcoliWiki:b2663 , Mint:MINT-1248489 , OU-Microarray:b2663 , PortEco:gabP , PR:PRO_000022740 , Pride:P25527 , Protein Model Portal:P25527 , RefSeq:NP_417149 , RegulonDB:EG11330 , SMR:P25527 , String:511145.b2663 , UniProt:P25527

Relationship Links: InterPro:IN-FAMILY:IPR002293 , InterPro:IN-FAMILY:IPR004840 , InterPro:IN-FAMILY:IPR004841 , InterPro:IN-FAMILY:IPR011265 , Panther:IN-FAMILY:PTHR11785 , Pfam:IN-FAMILY:PF00324 , Prosite:IN-FAMILY:PS00218

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0003333 - amino acid transmembrane transport Inferred by computational analysis [GOA01]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006865 - amino acid transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0009450 - gamma-aminobutyric acid catabolic process Inferred by computational analysis [UniProtGOA12]
GO:0015812 - gamma-aminobutyric acid transport Inferred by computational analysis [GOA01]
GO:0055085 - transmembrane transport Inferred by computational analysis [GOA01]
Molecular Function: GO:0015171 - amino acid transmembrane transporter activity Inferred by computational analysis [GOA01]
GO:0015185 - gamma-aminobutyric acid transmembrane transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell structure membrane
metabolism carbon utilization carbon compounds
transport Electrochemical potential driven transporters Porters (Uni-, Sym- and Antiporters)

Essentiality data for gabP 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]
Yes [Feist07, Comment 4]

Enzymatic reaction of: 4-aminobutyrate:H+ symporter

Synonyms: Transport of 4-aminobutyrate

Alternative Products for 4-aminobutanoate: 5-aminopentanoate [Brechtel96 ] , β-alanine [Brechtel96 ] , piperidine-3-carboxylate [Brechtel96 ]


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 21 -> 41
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 42 -> 62
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 72
[Metzer92, UniProt10]
Alternate sequence: T → R; UniProt: (in Ref. 2; CAA46229);
Transmembrane-Region 97 -> 117
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 119 -> 139
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 154 -> 174
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 200 -> 220
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 247 -> 267
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 287 -> 307
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 335 -> 355
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 360 -> 380
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 385 -> 386
[Metzer92, UniProt10]
Alternate sequence: MR → IG; UniProt: (in Ref. 2; CAA46229);
Transmembrane-Region 403 -> 423
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 429 -> 449
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2663 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11330; 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

Becker01a: Becker G, Hengge-Aronis R (2001). "What makes an Escherichia coli promoter sigma(S) dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigma(S)." Mol Microbiol 39(5);1153-65. PMID: 11251833

Brechtel96: Brechtel CE, Hu L, King SC (1996). "Substrate specificity of the Escherichia coli 4-aminobutyrate carrier encoded by gabP. Uptake and counterflow of structurally diverse molecules." J Biol Chem 1996;271(2);783-8. PMID: 8557687

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

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

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

Germer01: Germer J, Becker G, Metzner M, Hengge-Aronis R (2001). "Role of activator site position and a distal UP-element half-site for sigma factor selectivity at a CRP/H-NS-activated sigma(s)-dependent promoter in Escherichia coli." Mol Microbiol 41(3);705-16. PMID: 11532138

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

Hu98: Hu LA, King SC (1998). "Membrane topology of the Escherichia coli gamma-aminobutyrate transporter: implications on the topography and mechanism of prokaryotic and eukaryotic transporters from the APC superfamily." Biochem J 1998;336 ( Pt 1);69-76. PMID: 9806886

Hu98a: Hu LA, King SC (1998). "Functional significance of the "signature cysteine" in helix 8 of the Escherichia coli 4-aminobutyrate transporter from the amine-polyamine-choline superfamily. Restoration of Cys-300 to the Cys-less Gabp." J Biol Chem 1998;273(32);20162-7. PMID: 9685361

Jack00: Jack DL, Paulsen IT, Saier MH (2000). "The amino acid/polyamine/organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations." Microbiology 2000;146 ( Pt 8);1797-814. PMID: 10931886

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Marschall98: Marschall C, Labrousse V, Kreimer M, Weichart D, Kolb A, Hengge-Aronis R (1998). "Molecular analysis of the regulation of csiD, a carbon starvation-inducible gene in Escherichia coli that is exclusively dependent on sigma s and requires activation by cAMP-CRP." J Mol Biol 276(2);339-53. PMID: 9512707

Metzer79: Metzer E, Levitz R, Halpern YS (1979). "Isolation and properties of Escherichia coli K-12 mutants impaired in the utilization of gamma-aminobutyrate." J Bacteriol 137(3);1111-8. PMID: 374339

Metzer92: Metzer E., Halpern Y.S. (1992). Data submission to EMBL/GenBank/DDBJ databases on 1992-03.

Metzner04: Metzner M, Germer J, Hengge R (2004). "Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli." Mol Microbiol 51(3);799-811. PMID: 14731280

Niegemann93: Niegemann E, Schulz A, Bartsch K (1993). "Molecular organization of the Escherichia coli gab cluster: nucleotide sequence of the structural genes gabD and gabP and expression of the GABA permease gene." Arch Microbiol 1993;160(6);454-60. PMID: 8297211

Schneider02: Schneider BL, Ruback S, Kiupakis AK, Kasbarian H, Pybus C, Reitzer L (2002). "The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction." J Bacteriol 184(24);6976-86. PMID: 12446648

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

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

Zhang05g: Zhang W, Campbell HA, King SC, Dowhan W (2005). "Phospholipids as determinants of membrane protein topology. Phosphatidylethanolamine is required for the proper topological organization of the gamma-aminobutyric acid permease (GabP) of Escherichia coli." J Biol Chem 280(28);26032-8. PMID: 15890647

Other References Related to Gene Regulation

Zimmer00: Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S (2000). "Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation." Proc Natl Acad Sci U S A 97(26);14674-9. PMID: 11121068


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 Tue Nov 25, 2014, BIOCYC13A.