RegulonDB RegulonDB 10.9: Gene Form
   

amtB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

amtB tesB glnK

Gene      
Name: amtB    Texpresso search in the literature
Synonym(s): ECK0445, EG11821, b0451, ybaG
Genome position(nucleotides): 472966 --> 474252 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 56.18
Reference(s): [1] van Heeswijk WC., et al., 1996
External database links:  
ASAP:
 ABE-0001564
ECHOBASE:
 EB1768
ECOLIHUB:
 amtB
MIM:
 185000
MIM:
 268150
OU-MICROARRAY:
 b0451
STRING:
 511145.b0451
COLOMBOS: amtB


Shine dalgarno      
Sequence: acacagcaacAGGAACgaaaaATG


Product      
Name: ammonium transporter
Synonym(s): AmtB, AmtB ammonium Amt transporter, YbaG
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 44.515
Isoelectric point: 7.176
Motif(s):
 
Type Positions Sequence
64 -> 83 LSMLTQVTVTFALVCILWVV
33 -> 426 AFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVPEEQEREGLDVNSHGENAY
182 -> 182 D
220 -> 241 LPMVFTGTAILYIGWFGFNAGS
246 -> 275 NEIAALAFVNTVVATAAAILGWIFGEWALR

 
Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.2 - Electrochemical potential driven transporters --> 4.2.A - Porters (Uni-, Sym- and Antiporters)
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
GO:0008519 - ammonium transmembrane transporter activity
GO:0042802 - identical protein binding
biological_process GO:0019740 - nitrogen utilization
GO:0015696 - ammonium transport
GO:0015670 - carbon dioxide transport
GO:0072488 - ammonium transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [2] Boogerd FC., et al., 2011
[3] Bostick DL., et al., 2007
[4] Cao Z., et al., 2007
[5] Conroy MJ., et al., 2004
[6] Fong RN., et al., 2007
[7] Hall JA., et al., 2011
[8] Hall JA., et al., 2013
[9] Ishikita H., et al., 2007
[10] Javelle A., et al., 2006
[11] Jayakumar A., et al., 1985
[12] Jayakumar A., et al., 1987
[13] Khademi S., et al., 2006
[14] Kim M., et al., 2012
[15] Li XD., et al., 2006
[16] Lin Y., et al., 2006
[17] Ludewig U. 2006
[18] Luzhkov VB., et al., 2006
[19] Ma H., et al., 2009
[20] Merrick M., et al., 2006
[21] Neuhauser B., et al., 2014
[22] Nygaard TP., et al., 2006
[23] Radchenko MV., et al., 2010
[24] Severi E., et al., 2007
[25] Sipe SN., et al., 2020
[26] Tondervik A., et al., 2006
[27] Vo J., et al., 2013
[28] Wang J., et al., 2013
[29] Wang S., et al., 2012
[30] Yang H., et al., 2007
[1] van Heeswijk WC., et al., 1996
External database links:  
DIP:
 DIP-29874N
ECOCYC:
 AMTB-MONOMER
ECOLIWIKI:
 b0451
INTERPRO:
 IPR029020
INTERPRO:
 IPR024041
INTERPRO:
 IPR001905
INTERPRO:
 IPR018047
PDB:
 2NOW
PDB:
 6B21
PDB:
 3C1J
PDB:
 3C1I
PDB:
 3C1H
PDB:
 3C1G
PDB:
 2NUU
PDB:
 1U77
PDB:
 1U7C
PDB:
 1U7G
PDB:
 1XQE
PDB:
 1XQF
PDB:
 2NMR
PDB:
 2NOP
PDB:
 2NPC
PDB:
 2NPD
PDB:
 2NPE
PDB:
 2NPG
PDB:
 2NPJ
PDB:
 2NPK
PDB:
 2NS1
PFAM:
 PF00909
PRIDE:
 P69681
PRODB:
 PRO_000022100
PROSITE:
 PS01219
REFSEQ:
 NP_414985
SMR:
 P69681
UNIPROT:
 P69681


Operon      
Name: glnK-amtB         
Operon arrangement:
Transcription unit        Promoter
glnK-amtB


Transcriptional Regulation      
Display Regulation             
Activated by: GadX, FNR, Fur, NtrC
Repressed by: Fur, FNR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References


Reference(s)    

 [1] van Heeswijk WC., Hoving S., Molenaar D., Stegeman B., Kahn D., Westerhoff HV., 1996, An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli., Mol Microbiol 21(1):133-46

 [2] Boogerd FC., Ma H., Bruggeman FJ., van Heeswijk WC., Garcia-Contreras R., Molenaar D., Krab K., Westerhoff HV., 2011, AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3., FEBS Lett 585(1):23-8

 [3] Bostick DL., Brooks CL., 2007, On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel., Biophys J 92(12):L103-5

 [4] Cao Z., Mo Y., Thiel W., 2007, Deprotonation mechanism of NH4+ in the Escherichia coli ammonium transporter AmtB: insight from QM and QM/MM calculations., Angew Chem Int Ed Engl 46(36):6811-5

 [5] Conroy MJ., Jamieson SJ., Blakey D., Kaufmann T., Engel A., Fotiadis D., Merrick M., Bullough PA., 2004, Electron and atomic force microscopy of the trimeric ammonium transporter AmtB., EMBO Rep 5(12):1153-8

 [6] Fong RN., Kim KS., Yoshihara C., Inwood WB., Kustu S., 2007, The W148L substitution in the Escherichia coli ammonium channel AmtB increases flux and indicates that the substrate is an ion., Proc Natl Acad Sci U S A 104(47):18706-11

 [7] Hall JA., Kustu S., 2011, The pivotal twin histidines and aromatic triad of the Escherichia coli ammonium channel AmtB can be replaced., Proc Natl Acad Sci U S A 108(32):13270-4

 [8] Hall JA., Yan D., 2013, The molecular basis of K+ exclusion by the Escherichia coli ammonium channel AmtB., J Biol Chem 288(20):14080-6

 [9] Ishikita H., Knapp EW., 2007, Protonation states of ammonia/ammonium in the hydrophobic pore of ammonia transporter protein AmtB., J Am Chem Soc 129(5):1210-5

 [10] Javelle A., Lupo D., Zheng L., Li XD., Winkler FK., Merrick M., 2006, An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance., J Biol Chem 281(51):39492-8

 [11] Jayakumar A., Epstein W., Barnes EM., 1985, Characterization of ammonium (methylammonium)/potassium antiport in Escherichia coli., J Biol Chem 260(12):7528-32

 [12] Jayakumar A., Hong JS., Barnes EM., 1987, Feedback inhibition of ammonium (methylammonium) ion transport in Escherichia coli by glutamine and glutamine analogs., J Bacteriol 169(2):553-7

 [13] Khademi S., Stroud RM., 2006, The Amt/MEP/Rh family: structure of AmtB and the mechanism of ammonia gas conduction., Physiology (Bethesda) 21:419-29

 [14] Kim M., Zhang Z., Okano H., Yan D., Groisman A., Hwa T., 2012, Need-based activation of ammonium uptake in Escherichia coli., Mol Syst Biol 8:616

 [15] Li XD., Lupo D., Zheng L., Winkler F., 2006, Structural and functional insights into the AmtB/Mep/Rh protein family., Transfus Clin Biol 13(1-2):65-9

 [16] Lin Y., Cao Z., Mo Y., 2006, Molecular dynamics simulations on the Escherichia coli ammonia channel protein AmtB: mechanism of ammonia/ammonium transport., J Am Chem Soc 128(33):10876-84

 [17] Ludewig U., 2006, Ion transport versus gas conduction: function of AMT/Rh-type proteins., Transfus Clin Biol 13(1-2):111-6

 [18] Luzhkov VB., Almlof M., Nervall M., Aqvist J., 2006, Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB., Biochemistry 45(36):10807-14

 [19] Ma H., Boogerd FC., Goryanin I., 2009, Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration., J Biotechnol 144(3):175-83

 [20] Merrick M., Javelle A., Durand A., Severi E., Thornton J., Avent ND., Conroy MJ., Bullough PA., 2006, The Escherichia coli AmtB protein as a model system for understanding ammonium transport by Amt and Rh proteins., Transfus Clin Biol 13(1-2):97-102

 [21] Neuhauser B., Dynowski M., Ludewig U., 2014, Switching substrate specificity of AMT/MEP/ Rh proteins., Channels (Austin) 8(6):496-502

 [22] Nygaard TP., Rovira C., Peters GH., Jensen MO., 2006, Ammonium recruitment and ammonia transport by E. coli ammonia channel AmtB., Biophys J 91(12):4401-12

 [23] Radchenko MV., Thornton J., Merrick M., 2010, Control of AmtB-GlnK complex formation by intracellular levels of ATP, ADP, and 2-oxoglutarate., J Biol Chem 285(40):31037-45

 [24] Severi E., Javelle A., Merrick M., 2007, The conserved carboxy-terminal region of the ammonia channel AmtB plays a critical role in channel function., Mol Membr Biol 24(2):161-71

 [25] Sipe SN., Patrick JW., Laganowsky A., Brodbelt JS., 2020, Enhanced Characterization of Membrane Protein Complexes by Ultraviolet Photodissociation Mass Spectrometry., Anal Chem 92(1):899-907

 [26] Tondervik A., Torgersen HR., Botnmark HK., Strom AR., 2006, Transposon mutations in the 5' end of glnD, the gene for a nitrogen regulatory sensor, that suppress the osmosensitive phenotype caused by otsBA lesions in Escherichia coli., J Bacteriol 188(12):4218-26

 [27] Vo J., Inwood W., Hayes JM., Kustu S., 2013, Mechanism for nitrogen isotope fractionation during ammonium assimilation by Escherichia coli K12., Proc Natl Acad Sci U S A 110(21):8696-701

 [28] Wang J., Fulford T., Shao Q., Javelle A., Yang H., Zhu W., Merrick M., 2013, Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction., PLoS One 8(5):e62745

 [29] Wang S., Orabi EA., Baday S., Berneche S., Lamoureux G., 2012, Ammonium transporters achieve charge transfer by fragmenting their substrate., J Am Chem Soc 134(25):10419-27

 [30] Yang H., Xu Y., Zhu W., Chen K., Jiang H., 2007, Detailed mechanism for AmtB conducting NH4+/NH3: molecular dynamics simulations., Biophys J 92(3):877-85

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