RegulonDB RegulonDB 11.1: Gene Form
   

skp gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

bamA lpxD skp CpxR TSS_368 TSS_368 TSS_367 TSS_367 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

Gene      
Name: skp    Texpresso search in the literature
Synonym(s): ECK0177, EG10455, b0178, firA, hlpA, ompH
Genome position(nucleotides): 200482 --> 200967
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.21
External database links:  
ASAP:
 ABE-0000608
CGSC:
 18241
ECHOBASE:
 EB0450
ECOLIHUB:
 hlpA
OU-MICROARRAY:
 b0178
STRING:
 511145.b0178
COLOMBOS: skp


Product      
Name: periplasmic chaperone Skp
Synonym(s): FirA, HLP-I, HlpA, OmpH, Skp
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,periplasmic space,outer membrane
Molecular weight: 17.688
Isoelectric point: 10.452
Motif(s):
 
Type Positions Sequence Comment
1 -> 20 MKKWLLAAGLGLALATSAQA
15 -> 15 A UniProt: In Ref. 2; CAA53207..
19 -> 41 QAADKIAIVNMGSLFQQVAQKTG
21 -> 161 ADKIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQVK UniProt: Chaperone protein Skp.
23 -> 159 KIAIVNMGSLFQQVAQKTGVSNTLENEFKGRASELQRMETDLQAKMKKLQSMKAGSDRTKLEKDVMAQRQTFAQKAQAFEQDRARRSNEERGKLVTRIQTAVKSVANSQDIDLVVDANAVAYNSSDVKDITADVLKQ

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0009279 - cell outer membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0005515 - protein binding
GO:0051082 - unfolded protein binding
GO:0042802 - identical protein binding
GO:0001530 - lipopolysaccharide binding
biological_process GO:0006457 - protein folding
GO:0050821 - protein stabilization
GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly
GO:0032978 - protein insertion into membrane from inner side
GO:0022417 - protein maturation by protein folding
GO:0061077 - chaperone-mediated protein folding
Note(s): Note(s): ...[more].
Reference(s): [1] Aasland R., et al., 1988
[2] Bendiak DS., et al., 1981
[3] Denoncin K., et al., 2012
[4] Ernst F., et al., 1994
[5] Holdbrook DA., et al., 2017
[6] Lathe R. 1977
[7] Lathe R., et al., 1977
[8] Lathe R., et al., 1977
[9] Narayanan N., et al., null
[10] Patel GJ., et al., 2009
[11] Wang X., et al., 2021
[12] Weski J., et al., 2012
[13] Yamazaki K., et al., 1984
External database links:  
ALPHAFOLD:
 P0AEU7
DIP:
 DIP-36210N
ECOCYC:
 EG10455-MONOMER
ECOLIWIKI:
 b0178
INTERPRO:
 IPR005632
INTERPRO:
 IPR024930
PANTHER:
 PTHR35089
PDB:
 1U2M
PDB:
 1SG2
PFAM:
 PF03938
PRIDE:
 P0AEU7
PRODB:
 PRO_000023953
REFSEQ:
 NP_414720
SMART:
 SM00935
SMR:
 P0AEU7
SWISSMODEL:
 P0AEU7
UNIPROT:
 P0AEU7


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


Transcriptional Regulation      
Display Regulation             
Activated by: CpxR, GadE


Regulation by small RNA    
  Display Regulation
small RNA cpxQ


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_345 198507 forward nd [RS-EPT-CBR] [14]
  promoter TSS_346 198777 forward nd [RS-EPT-CBR] [14]
  promoter TSS_347 198782 forward nd [RS-EPT-CBR] [14]
  promoter TSS_348 (cluster) 198858 forward nd [RS-EPT-CBR] [14]
  promoter TSS_349 198875 forward nd [RS-EPT-CBR] [14]
  promoter TSS_350 (cluster) 198877 forward nd [RS-EPT-CBR] [14]
  promoter TSS_351 (cluster) 198881 forward nd [RS-EPT-CBR] [14]
  promoter TSS_352 198887 forward nd [RS-EPT-CBR] [14]
  promoter TSS_353 198889 forward nd [RS-EPT-CBR] [14]
  promoter TSS_354 198893 forward nd [RS-EPT-CBR] [14]
  promoter TSS_355 (cluster) 198908 forward nd [RS-EPT-CBR] [14]
  promoter TSS_356 199004 forward nd [RS-EPT-CBR] [14]
  promoter TSS_357 199007 forward nd [RS-EPT-CBR] [14]
  promoter TSS_358 199009 forward nd [RS-EPT-CBR] [14]
  promoter TSS_359 199012 forward nd [RS-EPT-CBR] [14]
  promoter TSS_360 199980 forward nd [RS-EPT-CBR] [14]
  promoter TSS_361 200131 forward nd [RS-EPT-CBR] [14]
  promoter TSS_362 (cluster) 200135 forward nd [RS-EPT-CBR] [14]
  promoter TSS_363 (cluster) 200138 forward nd [RS-EPT-CBR] [14]
  promoter TSS_364 200212 forward nd [RS-EPT-CBR] [14]
  promoter TSS_365 200317 forward nd [RS-EPT-CBR] [14]
  promoter TSS_366 200399 forward nd [RS-EPT-CBR] [14]
  promoter TSS_367 201749 forward nd [RS-EPT-CBR] [14]
  promoter TSS_368 201767 reverse nd [RS-EPT-CBR] [14]


Evidence    

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


Reference(s)    

 [1] Aasland R., Coleman J., Holck AL., Smith CL., Raetz CR., Kleppe K., 1988, Identity of the 17-kilodalton protein, a DNA-binding protein from Escherichia coli, and the firA gene product., J Bacteriol 170(12):5916-8

 [2] Bendiak DS., Friesen JD., 1981, Organization of genes in the four minute region of the Escherichia coli chromosome: evidence that rpsB and tsf are co-transcribed., Mol Gen Genet 181(3):356-62

 [3] Denoncin K., Schwalm J., Vertommen D., Silhavy TJ., Collet JF., 2012, Dissecting the Escherichia coli periplasmic chaperone network using differential proteomics., Proteomics 12(9):1391-401

 [4] Ernst F., Hoffschulte HK., Thome-Kromer B., Swidersky UE., Werner PK., Muller M., 1994, Precursor-specific requirements for SecA, SecB, and delta muH+ during protein export of Escherichia coli., J Biol Chem 269(17):12840-5

 [5] Holdbrook DA., Burmann BM., Huber RG., Petoukhov MV., Svergun DI., Hiller S., Bond PJ., 2017, A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone., Structure 25(7):1079-1088.e3

 [6] Lathe R., 1977, Fine-structure mapping of the firA gene, a locus involved in the phenotypic expression of rifampin resistance in Escherichia., J Bacteriol 131(3):1033-6

 [7] Lathe R., Lecocq JP., 1977, The firA gene, a locus involved in the expression of rifampicin resistance in Escherichia coli. II. Characterisation of bacterial proteins coded by lambdafirA transducing phages., Mol Gen Genet 154(1):53-60

 [8] Lathe R., Lecocq JP., 1977, The firA gene, a locus involved in the expression of rifampicin resistance in Escherichia coli. I. Characterisation of lambdafirA transducing phages constructed in vitro., Mol Gen Genet 154(1):43-51

 [9] Narayanan N., Chou CP., null, Physiological improvement to enhance Escherichia coli cell-surface display via reducing extracytoplasmic stress., Biotechnol Prog 24(2):293-301

 [10] Patel GJ., Behrens-Kneip S., Holst O., Kleinschmidt JH., 2009, The periplasmic chaperone Skp facilitates targeting, insertion, and folding of OmpA into lipid membranes with a negative membrane surface potential., Biochemistry 48(43):10235-45

 [11] Wang X., Peterson JH., Bernstein HD., 2021, Bacterial Outer Membrane Proteins Are Targeted to the Bam Complex by Two Parallel Mechanisms., mBio 12(3)

 [12] Weski J., Ehrmann M., 2012, Genetic analysis of 15 protein folding factors and proteases of the Escherichia coli cell envelope., J Bacteriol 194(12):3225-33

 [13] Yamazaki K., Nagata A., Kano Y., Imamoto F., 1984, Isolation and characterization of nucleoid proteins from Escherichia coli., Mol Gen Genet 196(2):217-24

 [14] 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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