RegulonDB RegulonDB 10.10: Gene Form
   

bamA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

bamA rseP skp CpxR lpxDp lpxDp hlpAp hlpAp TSS_366 TSS_366 TSS_365 TSS_365 TSS_364 TSS_364 TSS_363 (cluster) TSS_363 (cluster) TSS_362 (cluster) TSS_362 (cluster) TSS_361 TSS_361 TSS_360 TSS_360 TSS_359 TSS_359 TSS_358 TSS_358 TSS_357 TSS_357 TSS_356 TSS_356 TSS_355 (cluster) TSS_355 (cluster) TSS_354 TSS_354 TSS_353 TSS_353 TSS_352 TSS_352 TSS_351 (cluster) TSS_351 (cluster) TSS_350 (cluster) TSS_350 (cluster) TSS_349 TSS_349 TSS_348 (cluster) TSS_348 (cluster) TSS_347 TSS_347 TSS_346 TSS_346 TSS_345 TSS_345 TSS_344 TSS_344 bamAp bamAp TSS_343 TSS_343 TSS_342 TSS_342 TSS_341 (cluster) TSS_341 (cluster) bamAp2 bamAp2 TSS_339 TSS_339

Gene      
Name: bamA    Texpresso search in the literature
Synonym(s): ECK0176, G6093, b0177, ecfK, yaeT, yzzN, yzzY
Genome position(nucleotides): 197928 --> 200360 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.68
External database links:  
ASAP:
 ABE-0000605
ECHOBASE:
 EB2541
ECOLIHUB:
 bamA
OU-MICROARRAY:
 b0177
STRING:
 511145.b0177
COLOMBOS: bamA


Product      
Name: outer membrane protein assembly factor BamA
Synonym(s): BamA, EcfK, YaeT, YzzN, YzzY
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 90.553
Isoelectric point: 4.711
Motif(s):
 
Type Positions Sequence
494 -> 494 F
661 -> 661 R
771 -> 771 G
366 -> 366 R
430 -> 430 I

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0019867 - outer membrane
GO:0016020 - membrane
GO:0016021 - integral component of membrane
GO:1990063 - Bam protein complex
molecular_function GO:0005515 - protein binding
GO:0051082 - unfolded protein binding
biological_process GO:0007155 - cell adhesion
GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly
GO:0051205 - protein insertion into membrane
GO:0071709 - membrane assembly
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[APPHINH] Assay of protein purified to homogeneity from its native host
[IMP] Inferred from mutant phenotype
Reference(s): [1] Bayan N., et al., 2006
[2] Bredemeier R., et al., 2007
[3] Browning DF., et al., 2015
[4] Browning DF., et al., 2013
[5] Collin S., et al., 2007
[6] Ding Y., et al., 2020
[7] Doerner PA., et al., 2017
[8] Fleming PJ., et al., 2016
[9] Hagan CL., et al., 2010
[10] Han L., et al., 2016
[11] Lee J., et al., 2019
[12] Leonard-Rivera M., et al., 2012
[13] Liu J., et al., 2020
[14] Morgado L., et al., 2015
[15] Ni D., et al., 2014
[16] Pinto C., et al., 2018
[17] Plummer AM., et al., 2015
[18] Ricci DP., et al., 2012
[19] Rigel NW., et al., 2012
[20] Rodriguez-Alonso R., et al., 2020
[21] Sinnige T., et al., 2015
[22] Sklar JG., et al., 2007
[23] Stegmeier JF., et al., 2007
[24] Tellez R., et al., 2012
[25] Thoma J., et al., 2018
[26] Ward R., et al., 2009
[27] Workman P., et al., 2012
[28] Wu T., et al., 2005
External database links:  
DIP:
 DIP-36019N
ECOCYC:
 G6093-MONOMER
ECOLIWIKI:
 b0177
INTERPRO:
 IPR000184
INTERPRO:
 IPR010827
INTERPRO:
 IPR023707
INTERPRO:
 IPR034746
INTERPRO:
 IPR039910
PANTHER:
 PTHR12815:SF23
PANTHER:
 PTHR12815
PDB:
 5D0Q
PDB:
 5D0O
PDB:
 5LJO
PDB:
 5EKQ
PDB:
 2V9H
PDB:
 2qcz
PDB:
 2qdf
PDB:
 3EFC
PDB:
 3OG5
PDB:
 3Q6B
PDB:
 4C4V
PDB:
 4N75
PDB:
 4PK1
PDB:
 4XGA
PDB:
 5AYW
PDB:
 6T1W
PFAM:
 PF07244
PFAM:
 PF01103
PRIDE:
 P0A940
PROSITE:
 PS51779
REFSEQ:
 NP_414719
SMR:
 P0A940
UNIPROT:
 P0A940


Operon      
Name: bamA-skp-lpxD-fabZ-lpxAB-rnhB-dnaE         
Operon arrangement:
Transcription unit        Promoter
bamA-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE
bamA
hlpA-lpxD-fabZ-lpxA
lpxD
fabZ


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
  promoter TSS_339 196978 forward nd [RS-EPT-CBR] [29]
  promoter TSS_341 (cluster) 197487 forward nd [RS-EPT-CBR] [29]
  promoter TSS_342 197586 forward nd [RS-EPT-CBR] [29]
  promoter TSS_343 197588 reverse nd [RS-EPT-CBR] [29]
  promoter TSS_344 197883 forward nd [RS-EPT-CBR] [29]
  promoter TSS_345 198507 forward nd [RS-EPT-CBR] [29]
  promoter TSS_346 198777 forward nd [RS-EPT-CBR] [29]
  promoter TSS_347 198782 forward nd [RS-EPT-CBR] [29]
  promoter TSS_348 (cluster) 198858 forward nd [RS-EPT-CBR] [29]
  promoter TSS_349 198875 forward nd [RS-EPT-CBR] [29]
  promoter TSS_350 (cluster) 198877 forward nd [RS-EPT-CBR] [29]
  promoter TSS_351 (cluster) 198881 forward nd [RS-EPT-CBR] [29]
  promoter TSS_352 198887 forward nd [RS-EPT-CBR] [29]
  promoter TSS_353 198889 forward nd [RS-EPT-CBR] [29]
  promoter TSS_354 198893 forward nd [RS-EPT-CBR] [29]
  promoter TSS_355 (cluster) 198908 forward nd [RS-EPT-CBR] [29]
  promoter TSS_356 199004 forward nd [RS-EPT-CBR] [29]
  promoter TSS_357 199007 forward nd [RS-EPT-CBR] [29]
  promoter TSS_358 199009 forward nd [RS-EPT-CBR] [29]
  promoter TSS_359 199012 forward nd [RS-EPT-CBR] [29]
  promoter TSS_360 199980 forward nd [RS-EPT-CBR] [29]
  promoter TSS_361 200131 forward nd [RS-EPT-CBR] [29]
  promoter TSS_362 (cluster) 200135 forward nd [RS-EPT-CBR] [29]
  promoter TSS_363 (cluster) 200138 forward nd [RS-EPT-CBR] [29]
  promoter TSS_364 200212 forward nd [RS-EPT-CBR] [29]
  promoter TSS_365 200317 forward nd [RS-EPT-CBR] [29]
  promoter TSS_366 200399 forward nd [RS-EPT-CBR] [29]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Bayan N., Guilvout I., Pugsley AP., 2006, Secretins take shape., Mol Microbiol 60(1):1-4

 [2] Bredemeier R., Schlegel T., Ertel F., Vojta A., Borissenko L., Bohnsack MT., Groll M., von Haeseler A., Schleiff E., 2007, Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family., J Biol Chem 282(3):1882-90

 [3] Browning DF., Bavro VN., Mason JL., Sevastsyanovich YR., Rossiter AE., Jeeves M., Wells TJ., Knowles TJ., Cunningham AF., Donald JW., Palmer T., Overduin M., Henderson IR., 2015, Cross-species chimeras reveal BamA POTRA and β-barrel domains must be fine-tuned for efficient OMP insertion., Mol Microbiol

 [4] Browning DF., Matthews SA., Rossiter AE., Sevastsyanovich YR., Jeeves M., Mason JL., Wells TJ., Wardius CA., Knowles TJ., Cunningham AF., Bavro VN., Overduin M., Henderson IR., 2013, Mutational and topological analysis of the Escherichia coli BamA protein., PLoS One 8(12):e84512

 [5] Collin S., Guilvout I., Chami M., Pugsley AP., 2007, YaeT-independent multimerization and outer membrane association of secretin PulD., Mol Microbiol 64(5):1350-7

 [6] Ding Y., Shiota T., Le Brun AP., Dunstan RA., Wang B., Hsu HY., Lithgow T., Shen HH., 2020, Characterization of BamA reconstituted into a solid-supported lipid bilayer as a platform for measuring dynamics during substrate protein assembly into the membrane., Biochim Biophys Acta Biomembr 1862(9):183317

 [7] Doerner PA., Sousa MC., 2017, Extreme Dynamics in the BamA β-Barrel Seam., Biochemistry 56(24):3142-3149

 [8] Fleming PJ., Patel DS., Wu EL., Qi Y., Yeom MS., Sousa MC., Fleming KG., Im W., 2016, BamA POTRA Domain Interacts with a Native Lipid Membrane Surface., Biophys J 110(12):2698-2709

 [9] Hagan CL., Kim S., Kahne D., 2010, Reconstitution of outer membrane protein assembly from purified components., Science 328(5980):890-2

 [10] Han L., Zheng J., Wang Y., Yang X., Liu Y., Sun C., Cao B., Zhou H., Ni D., Lou J., Zhao Y., Huang Y., 2016, Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins., Nat Struct Mol Biol 23(3):192-6

 [11] Lee J., Tomasek D., Santos TM., May MD., Meuskens I., Kahne D., 2019, Formation of a β-barrel membrane protein is catalyzed by the interior surface of the assembly machine protein BamA., Elife 8

 [12] Leonard-Rivera M., Misra R., 2012, Conserved residues of the putative L6 loop of Escherichia coli BamA play a critical role in the assembly of β-barrel outer membrane proteins, including BamA itself., J Bacteriol

 [13] Liu J., Gumbart JC., 2020, Membrane thinning and lateral gating are consistent features of BamA across multiple species., PLoS Comput Biol 16(10):e1008355

 [14] Morgado L., Zeth K., Burmann BM., Maier T., Hiller S., 2015, Characterization of the insertase BamA in three different membrane mimetics by solution NMR spectroscopy., J Biomol NMR 61(3-4):333-45

 [15] Ni D., Yang K., Huang Y., 2014, Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis., Acta Crystallogr F Struct Biol Commun 70(Pt 3):362-5

 [16] Pinto C., Mance D., Sinnige T., Daniels M., Weingarth M., Baldus M., 2018, Formation of the β-barrel assembly machinery complex in lipid bilayers as seen by solid-state NMR., Nat Commun 9(1):4135

 [17] Plummer AM., Fleming KG., 2015, BamA Alone Accelerates Outer Membrane Protein Folding In Vitro through a Catalytic Mechanism., Biochemistry 54(39):6009-11

 [18] Ricci DP., Hagan CL., Kahne D., Silhavy TJ., 2012, Activation of the Escherichia coli β-barrel assembly machine (Bam) is required for essential components to interact properly with substrate., Proc Natl Acad Sci U S A 109(9):3487-91

 [19] Rigel NW., Schwalm J., Ricci DP., Silhavy TJ., 2012, BamE modulates the Escherichia coli beta-barrel assembly machine component BamA., J Bacteriol 194(5):1002-8

 [20] Rodriguez-Alonso R., Letoquart J., Nguyen VS., Louis G., Calabrese AN., Iorga BI., Radford SE., Cho SH., Remaut H., Collet JF., 2020, Structural insight into the formation of lipoprotein-β-barrel complexes., Nat Chem Biol 16(9):1019-1025

 [21] Sinnige T., Houben K., Pritisanac I., Renault M., Boelens R., Baldus M., 2015, Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach., J Biomol NMR 61(3-4):321-32

 [22] Sklar JG., Wu T., Gronenberg LS., Malinverni JC., Kahne D., Silhavy TJ., 2007, Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli., Proc Natl Acad Sci U S A 104(15):6400-5

 [23] Stegmeier JF., Gluck A., Sukumaran S., Mantele W., Andersen C., 2007, Characterisation of YtfM, a second member of the Omp85 family in Escherichia coli., Biol Chem 388(1):37-46

 [24] Tellez R., Misra R., 2012, Substitutions in the BamA β-barrel domain overcome the conditional lethal phenotype of a ΔbamB ΔbamE strain of Escherichia coli., J Bacteriol 194(2):317-24

 [25] Thoma J., Manioglu S., Kalbermatter D., Bosshart PD., Fotiadis D., Muller DJ., 2018, Protein-enriched outer membrane vesicles as a native platform for outer membrane protein studies., Commun Biol 1:23

 [26] Ward R., Zoltner M., Beer L., El Mkami H., Henderson IR., Palmer T., Norman DG., 2009, The orientation of a tandem POTRA domain pair, of the beta-barrel assembly protein BamA, determined by PELDOR spectroscopy., Structure 17(9):1187-94

 [27] Workman P., Heide K., Giuliano N., Lee N., Mar J., Vuong P., Bennion D., Misra R., 2012, Genetic, biochemical, and molecular characterization of the polypeptide transport-associated domain of Escherichia coli BamA., J Bacteriol 194(13):3512-21

 [28] Wu T., Malinverni J., Ruiz N., Kim S., Silhavy TJ., Kahne D., 2005, Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli., Cell 121(2):235-45

 [29] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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