RegulonDB RegulonDB 10.8: Gene Form
   

ompA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ompA sulA matP RcdA RcdA CRP RseX MicA anti-anti-terminator anti-terminator terminator TSS_1282 TSS_1282 ompAp1 ompAp1 ompAp2 ompAp2 TSS_1280 TSS_1280 TSS_1279 TSS_1279 TSS_1278 TSS_1278 TSS_1277 TSS_1277 TSS_1276 TSS_1276 TSS_1275 TSS_1275 TSS_1274 TSS_1274 TSS_1273 TSS_1273 TSS_1272 TSS_1272 TSS_1271 TSS_1271 TSS_1270 TSS_1270 TSS_1269 TSS_1269 TSS_1268 TSS_1268 TSS_1267 TSS_1267 TSS_1266 TSS_1266 TSS_1265 TSS_1265 TSS_1264 TSS_1264 TSS_1263 TSS_1263 TSS_1262 TSS_1262 TSS_1261 TSS_1261

Gene      
Name: ompA    Texpresso search in the literature
Synonym(s): ECK0948, EG10669, b0957, con, tolG, tut
Genome position(nucleotides): 1019013 <-- 1020053 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.79
Reference(s): [1] Chen R., et al., 1980
External database links:  
ASAP:
 ABE-0003240
CGSC:
 437
ECHOBASE:
 EB0663
OU-MICROARRAY:
 b0957
PortEco:
 ompA
STRING:
 511145.b0957
COLOMBOS: ompA


Product      
Name: outer membrane protein A
Synonym(s): Con, OmpA, TolG, Tut, outer membrane protein 3a, outer membrane protein d, outer membrane protein B, outer membrane protein D, outer membrane protein II*, outer membrane protein O-10, polypeptide II*, protein II*
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,outer membrane
Molecular weight: 37.201
Isoelectric point: 6.364
Motif(s):
 
Type Positions Sequence
22 -> 346 APKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFGQGEAAPVVAPAPAPAPEVQTKHFTLKSDVLFNFNKATLKPEGQAALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSERRAQSVVDYLISKGIPADKISARGMGESNPVTGNTCDNVKQRAALIDCLAPDRRVEIEVKGIKDVVTQPQA
73 -> 103 EMGYDWLGRMPYKGSVENGAYKAQGVQLTAK
112 -> 120 LDIYTRLGG
183 -> 188 LSLGVS
207 -> 208 AP

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0106234 - outer membrane protein complex
GO:0009279 - cell outer membrane
GO:0019867 - outer membrane
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0016021 - integral component of membrane
GO:0045203 - integral component of cell outer membrane
GO:0046930 - pore complex
molecular_function GO:0005515 - protein binding
GO:0015075 - ion transmembrane transporter activity
GO:0015288 - porin activity
GO:0042802 - identical protein binding
GO:0042834 - peptidoglycan binding
biological_process GO:0006811 - ion transport
GO:0006974 - cellular response to DNA damage stimulus
GO:0016032 - viral process
GO:0000746 - conjugation
GO:0009597 - detection of virus
GO:0046718 - viral entry into host cell
Note(s): Note(s): ...[more].
Reference(s): [2] Baars L., et al., 2006
[3] Bardwell JC., et al., 1991
[4] Bond PJ., et al., 2002
[5] Bremer E., et al., 1982
[6] Burgess NK., et al., 2008
[7] Chorev DS., et al., 2018
[8] Cierpicki T., et al., 2006
[9] Cole ST., et al., 1982
[10] Crooke E., et al., 1988
[11] Danoff EJ., et al., 2011
[12] Danoff EJ., et al., 2015
[13] Ebie Tan A., et al., 2010
[14] Freudl R., et al., 1988
[15] Hobom G., et al., 1995
[16] Hong H., et al., 2007
[17] Hong H., et al., 2013
[18] Johansson MU., et al., 2007
[19] Khalid S., et al., 2008
[20] Klose M., et al., 1993
[21] MacIntyre S., et al., 1987
[22] MacIntyre S., et al., 1988
[23] Muela A., et al., 2008
[24] Nedergaard Pedersen J., et al., 2018
[25] Nikaido H., et al., 1984
[26] Nishiyama K., et al., 2010
[27] Patel GJ., et al., 2013
[28] Ried G., et al., 1990
[29] Ried G., et al., 1994
[30] Ried G., et al., 1990
[31] Sanchez KM., et al., 2008
[32] Sanchez KM., et al., 2011
[33] Stathopoulos C. 1996
[34] Sugawara E., et al., 1996
[35] Tang Y., et al., 2010
[36] Tani K., et al., 1989
[37] Tani K., et al., 1990
[38] Verhoeven GS., et al., 2013
[39] Vogel H., et al., 1986
[40] Woodruff WA., et al., 1989
[41] Zhou Q., et al., 2012
External database links:  
DIP:
 DIP-31879N
ECOCYC:
 EG10669-MONOMER
ECOLIWIKI:
 b0957
INTERPRO:
 IPR000498
INTERPRO:
 IPR036737
INTERPRO:
 IPR011250
INTERPRO:
 IPR006690
INTERPRO:
 IPR006665
INTERPRO:
 IPR006664
INTERPRO:
 IPR002368
MINT:
 P0A910
MODBASE:
 P0A910
PDB:
 5M2Q
PDB:
 3JBU
PDB:
 2JMM
PDB:
 2MQE
PDB:
 1BXW
PDB:
 1G90
PDB:
 1QJP
PDB:
 2GE4
PFAM:
 PF00691
PFAM:
 PF01389
PRIDE:
 P0A910
PRINTS:
 PR01021
PRINTS:
 PR01022
PRODB:
 PRO_000023450
PROSITE:
 PS01068
PROSITE:
 PS51123
REFSEQ:
 NP_415477
SMR:
 P0A910
SWISSMODEL:
 P0A910
UNIPROT:
 P0A910


Operon      
Name: ompA         
Operon arrangement:
Transcription unit        Promoter
ompA
ompA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


RNA cis-regulatory element    
Attenuation: Transcriptional


Regulation by small RNA    
  Display Regulation
small RNA rseX, micA


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_1261 1019168 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1262 1019186 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1263 1019190 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1264 1019205 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1265 1019248 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1266 1019250 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1267 1019362 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1268 1019382 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1269 1019401 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1270 1019732 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1271 1019778 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1272 1019848 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1273 1019850 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1274 1019917 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1275 1019929 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1276 1019931 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1277 1019980 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1278 1020044 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1279 1020049 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1280 1020184 reverse nd [RS-EPT-CBR] [42]
  promoter TSS_1282 1020205 reverse nd [RS-EPT-CBR] [42]


Evidence    

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


Reference(s)    

 [1] Chen R., Schmidmayr W., Kramer C., Chen-Schmeisser U., Henning U., 1980, Primary structure of major outer membrane protein II (ompA protein) of Escherichia coli K-12., Proc Natl Acad Sci U S A 77(8):4592-6

 [2] Baars L., Ytterberg AJ., Drew D., Wagner S., Thilo C., van Wijk KJ., de Gier JW., 2006, Defining the role of the Escherichia coli chaperone SecB using comparative proteomics., J Biol Chem 281(15):10024-34

 [3] Bardwell JC., McGovern K., Beckwith J., 1991, Identification of a protein required for disulfide bond formation in vivo., Cell 67(3):581-9

 [4] Bond PJ., Faraldo-Gomez JD., Sansom MS., 2002, OmpA: a pore or not a pore? Simulation and modeling studies., Biophys J 83(2):763-75

 [5] Bremer E., Cole ST., Hindennach I., Henning U., Beck E., Kurz C., Schaller H., 1982, Export of a protein into the outer membrane of Escherichia coli K12. Stable incorporation of the OmpA protein requires less than 193 amino-terminal amino-acid residues., Eur J Biochem 122(1):223-31

 [6] Burgess NK., Dao TP., Stanley AM., Fleming KG., 2008, Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro., J Biol Chem 283(39):26748-58

 [7] Chorev DS., Baker LA., Wu D., Beilsten-Edmands V., Rouse SL., Zeev-Ben-Mordehai T., Jiko C., Samsudin F., Gerle C., Khalid S., Stewart AG., Matthews SJ., Grunewald K., Robinson CV., 2018, Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry., Science 362(6416):829-834

 [8] Cierpicki T., Liang B., Tamm LK., Bushweller JH., 2006, Increasing the accuracy of solution NMR structures of membrane proteins by application of residual dipolar couplings. High-resolution structure of outer membrane protein A., J Am Chem Soc 128(21):6947-51

 [9] Cole ST., Bremer E., Hindennach I., Henning U., 1982, Characterisation of the promoters for the ompA gene which encodes a major outer membrane protein of Escherichia coli., Mol Gen Genet 188(3):472-9

 [10] Crooke E., Brundage L., Rice M., Wickner W., 1988, ProOmpA spontaneously folds in a membrane assembly competent state which trigger factor stabilizes., EMBO J 7(6):1831-5

 [11] Danoff EJ., Fleming KG., 2011, The soluble, periplasmic domain of OmpA folds as an independent unit and displays chaperone activity by reducing the self-association propensity of the unfolded OmpA transmembrane β-barrel., Biophys Chem 159(1):194-204

 [12] Danoff EJ., Fleming KG., 2015, Aqueous, Unfolded OmpA Forms Amyloid-Like Fibrils upon Self-Association., PLoS One 10(7):e0132301

 [13] Ebie Tan A., Burgess NK., DeAndrade DS., Marold JD., Fleming KG., 2010, Self-association of unfolded outer membrane proteins., Macromol Biosci 10(7):763-7

 [14] Freudl R., MacIntyre S., Degen M., Henning U., 1988, Alterations to the signal peptide of an outer membrane protein (OmpA) of Escherichia coli K-12 can promote either the cotranslational or the posttranslational mode of processing., J Biol Chem 263(1):344-9

 [15] Hobom G., Arnold N., Ruppert A., 1995, OmpA fusion proteins for presentation of foreign antigens on the bacterial outer membrane., Dev Biol Stand 84:255-62

 [16] Hong H., Park S., Jimenez RH., Rinehart D., Tamm LK., 2007, Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins., J Am Chem Soc 129(26):8320-7

 [17] Hong H., Rinehart D., Tamm LK., 2013, Membrane depth-dependent energetic contribution of the tryptophan side chain to the stability of integral membrane proteins., Biochemistry 52(25):4413-21

 [18] Johansson MU., Alioth S., Hu K., Walser R., Koebnik R., Pervushin K., 2007, A minimal transmembrane beta-barrel platform protein studied by nuclear magnetic resonance., Biochemistry 46(5):1128-40

 [19] Khalid S., Bond PJ., Carpenter T., Sansom MS., 2008, OmpA: gating and dynamics via molecular dynamics simulations., Biochim Biophys Acta 1778(9):1871-80

 [20] Klose M., Storiko A., Stierhof YD., Hindennach I., Mutschler B., Henning U., 1993, Membrane assembly of the outer membrane protein OmpA of Escherichia coli., J Biol Chem 268(34):25664-70

 [21] MacIntyre S., Freudl R., Degen M., Hindennach I., Henning U., 1987, The signal sequence of an Escherichia coli outer membrane protein can mediate translocation of a not normally secreted protein across the plasma membrane., J Biol Chem 262(17):8416-22

 [22] MacIntyre S., Freudl R., Eschbach ML., Henning U., 1988, An artificial hydrophobic sequence functions as either an anchor or a signal sequence at only one of two positions within the Escherichia coli outer membrane protein OmpA., J Biol Chem 263(35):19053-9

 [23] Muela A., Seco C., Camafeita E., Arana I., Orruno M., Lopez JA., Barcina I., 2008, Changes in Escherichia coli outer membrane subproteome under environmental conditions inducing the viable but nonculturable state., FEMS Microbiol Ecol 64(1):28-36

 [24] Nedergaard Pedersen J., Skov Pedersen J., Otzen DE., 2018, Liprotides assist in folding of outer membrane proteins., Protein Sci 27(2):451-462

 [25] Nikaido H., Wu HC., 1984, Amino acid sequence homology among the major outer membrane proteins of Escherichia coli., Proc Natl Acad Sci U S A 81(4):1048-52

 [26] Nishiyama K., Tokuda H., 2010, Preparation of a highly translocation-competent proOmpA/SecB complex., Protein Sci 19(12):2402-8

 [27] Patel GJ., Kleinschmidt JH., 2013, The lipid bilayer-inserted membrane protein BamA of Escherichia coli facilitates insertion and folding of outer membrane protein A from its complex with Skp., Biochemistry 52(23):3974-86

 [28] Ried G., Hindennach I., Henning U., 1990, Role of lipopolysaccharide in assembly of Escherichia coli outer membrane proteins OmpA, OmpC, and OmpF., J Bacteriol 172(10):6048-53

 [29] Ried G., Koebnik R., Hindennach I., Mutschler B., Henning U., 1994, Membrane topology and assembly of the outer membrane protein OmpA of Escherichia coli K12., Mol Gen Genet 243(2):127-35

 [30] Ried G., MacIntyre S., Mutschler B., Henning U., 1990, Export of altered forms of an Escherichia coli K-12 outer membrane protein (OmpA) can inhibit synthesis of unrelated outer membrane proteins., J Mol Biol 216(1):39-47

 [31] Sanchez KM., Gable JE., Schlamadinger DE., Kim JE., 2008, Effects of tryptophan microenvironment, soluble domain, and vesicle size on the thermodynamics of membrane protein folding: lessons from the transmembrane protein OmpA., Biochemistry 47(48):12844-52

 [32] Sanchez KM., Kang G., Wu B., Kim JE., 2011, Tryptophan-lipid interactions in membrane protein folding probed by ultraviolet resonance Raman and fluorescence spectroscopy., Biophys J 100(9):2121-30

 [33] Stathopoulos C., 1996, An alternative topological model for Escherichia coli OmpA., Protein Sci 5(1):170-3

 [34] Sugawara E., Steiert M., Rouhani S., Nikaido H., 1996, Secondary structure of the outer membrane proteins OmpA of Escherichia coli and OprF of Pseudomonas aeruginosa., J Bacteriol 178(20):6067-9

 [35] Tang Y., Pan X., Tai PC., Sui SF., 2010, The structure of SecB/OmpA as visualized by electron microscopy: The mature region of the precursor protein binds asymmetrically to SecB., Biochem Biophys Res Commun 393(4):698-702

 [36] Tani K., Shiozuka K., Tokuda H., Mizushima S., 1989, In vitro analysis of the process of translocation of OmpA across the Escherichia coli cytoplasmic membrane. A translocation intermediate accumulates transiently in the absence of the proton motive force., J Biol Chem 264(31):18582-8

 [37] Tani K., Tokuda H., Mizushima S., 1990, Translocation of ProOmpA possessing an intramolecular disulfide bridge into membrane vesicles of Escherichia coli. Effect of membrane energization., J Biol Chem 265(28):17341-7

 [38] Verhoeven GS., Dogterom M., den Blaauwen T., 2013, Absence of long-range diffusion of OmpA in E. coli is not caused by its peptidoglycan binding domain., BMC Microbiol 13:66

 [39] Vogel H., Jahnig F., 1986, Models for the structure of outer-membrane proteins of Escherichia coli derived from raman spectroscopy and prediction methods., J Mol Biol 190(2):191-9

 [40] Woodruff WA., Hancock RE., 1989, Pseudomonas aeruginosa outer membrane protein F: structural role and relationship to the Escherichia coli OmpA protein., J Bacteriol 171(6):3304-9

 [41] Zhou Q., Sun S., Tai P., Sui SF., 2012, Structural characterization of the complex of SecB and metallothionein-labeled proOmpA by cryo-electron microscopy., PLoS One 7(10):e47015

 [42] 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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