RegulonDB RegulonDB 11.1: Gene Form
   

lepB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lepA lepB rnc era Cis-reg TSS_2866 TSS_2866 lepBp1 lepBp1 rncp rncp TSS_2865 (cluster) TSS_2865 (cluster) TSS_2864 TSS_2864 TSS_2863 TSS_2863 TSS_2862 TSS_2862 TSS_2861 TSS_2861 TSS_2860 (cluster) TSS_2860 (cluster) TSS_2859 TSS_2859 TSS_2858 TSS_2858

Gene      
Name: lepB    Texpresso search in the literature
Synonym(s): ECK2566, EG10530, b2568, lep
Genome position(nucleotides): 2704335 <-- 2705309
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.0
External database links:  
ASAP:
 ABE-0008450
CGSC:
 573
ECHOBASE:
 EB0525
ECOLIHUB:
 lepB
OU-MICROARRAY:
 b2568
STRING:
 511145.b2568
COLOMBOS: lepB


Product      
Name: signal peptidase I
Synonym(s): LP1, Lep, LepB, SPase I, leader peptidase (signal peptidase I)
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 35.96
Isoelectric point: 7.424
Motif(s):
 
Type Positions Sequence Comment
4 -> 22 MFALILVIATLVTGILWCV UniProt: Helical.
42 -> 43 AG UniProt: In Ref. 1 and 2..
59 -> 77 GWLETGASVFPVLAIVLIV UniProt: Helical.
60 -> 302 WLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWM
62 -> 62 E UniProt: Indifferent..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.5 - export, signal peptide cleavage
  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:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0004175 - endopeptidase activity
GO:0004252 - serine-type endopeptidase activity
GO:0008236 - serine-type peptidase activity
biological_process GO:0006508 - proteolysis
GO:0016485 - protein processing
GO:0006465 - signal peptide processing
Note(s): Note(s): ...[more].
Reference(s): [1] Auclair SM., et al., 2012
[2] Carlos JL., et al., 2000
[3] Choo KH., et al., 2008
[4] De Rosa M., et al., 2017
[5] Dev IK., et al., 1990
[6] Fikes JD., et al., 1990
[7] Inada T., et al., 1989
[8] Karla A., et al., 2005
[9] Kim YT., et al., 2004
[10] Kim YT., et al., 2008
[11] Klenotic PA., et al., 2000
[12] Moore KE., et al., 1987
[13] Musial-Siwek M., et al., 2008
[14] Musik JE., et al., 2021
[15] Ohno-Iwashita Y., et al., 1984
[16] Sandhu H., et al., 2021
[17] Stein RL., et al., 2000
[18] Tschantz WR., et al., 1993
[19] Tuteja R. 2005
[20] Wang Y., et al., 2004
External database links:  
ALPHAFOLD:
 P00803
ECOCYC:
 EG10530-MONOMER
ECOLIWIKI:
 b2568
INTERPRO:
 IPR036286
INTERPRO:
 IPR019756
INTERPRO:
 IPR000223
INTERPRO:
 IPR019533
INTERPRO:
 IPR019758
INTERPRO:
 IPR019757
MODBASE:
 P00803
PANTHER:
 PTHR43390
PDB:
 6B88
PDB:
 3S04
PDB:
 3IIQ
PDB:
 1T7D
PDB:
 1B12
PDB:
 1KN9
PFAM:
 PF10502
PRIDE:
 P00803
PRINTS:
 PR00727
PRODB:
 PRO_000023080
PROSITE:
 PS00761
PROSITE:
 PS00501
PROSITE:
 PS00760
REFSEQ:
 NP_417063
SMR:
 P00803
UNIPROT:
 P00803


Operon      
Name: lepAB         
Operon arrangement:
Transcription unit        Promoter
lepAB


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_2858 2703503 reverse nd [RS-EPT-CBR] [21]
  promoter TSS_2859 2704008 reverse nd [RS-EPT-CBR] [21]
  promoter TSS_2860 (cluster) 2704016 reverse nd [RS-EPT-CBR] [21]
  promoter TSS_2861 2704074 reverse nd [RS-EPT-CBR] [21]
  promoter TSS_2862 2704076 reverse nd [RS-EPT-CBR] [21]
  promoter TSS_2863 2704093 reverse nd [RS-EPT-CBR] [21]
  promoter TSS_2864 2704101 reverse nd [RS-EPT-CBR] [21]
  promoter TSS_2865 (cluster) 2704183 reverse nd [RS-EPT-CBR] [21]
  promoter lepBp1 2705464 reverse nd [COMP-AINF] [22]
  promoter TSS_2866 2706051 reverse nd [RS-EPT-CBR] [21]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Auclair SM., Bhanu MK., Kendall DA., 2012, Signal peptidase I: cleaving the way to mature proteins., Protein Sci 21(1):13-25

 [2] Carlos JL., Paetzel M., Brubaker G., Karla A., Ashwell CM., Lively MO., Cao G., Bullinger P., Dalbey RE., 2000, The role of the membrane-spanning domain of type I signal peptidases in substrate cleavage site selection., J Biol Chem 275(49):38813-22

 [3] Choo KH., Tong JC., Ranganathan S., 2008, Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage., BMC Bioinformatics 9 Suppl 1:S15

 [4] De Rosa M., Lu L., Zamaratski E., Szalaj N., Cao S., Wadensten H., Lenhammar L., Gising J., Roos AK., Huseby DL., Larsson R., Andren PE., Hughes D., Brandt P., Mowbray SL., Karlen A., 2017, Design, synthesis and in vitro biological evaluation of oligopeptides targeting E. coli type I signal peptidase (LepB)., Bioorg Med Chem 25(3):897-911

 [5] Dev IK., Ray PH., Novak P., 1990, Minimum substrate sequence for signal peptidase I of Escherichia coli., J Biol Chem 265(33):20069-72

 [6] Fikes JD., Barkocy-Gallagher GA., Klapper DG., Bassford PJ., 1990, Maturation of Escherichia coli maltose-binding protein by signal peptidase I in vivo. Sequence requirements for efficient processing and demonstration of an alternate cleavage site., J Biol Chem 265(6):3417-23

 [7] Inada T., Court DL., Ito K., Nakamura Y., 1989, Conditionally lethal amber mutations in the leader peptidase gene of Escherichia coli., J Bacteriol 171(1):585-7

 [8] Karla A., Lively MO., Paetzel M., Dalbey R., 2005, The identification of residues that control signal peptidase cleavage fidelity and substrate specificity., J Biol Chem 280(8):6731-41

 [9] Kim YT., Kurita R., Kojima M., Nishii W., Tanokura M., Muramatsu T., Ito H., Takahashi K., 2004, Identification of arginine residues important for the activity of Escherichia coli signal peptidase I., Biol Chem 385(5):381-8

 [10] Kim YT., Yoshida H., Kojima M., Kurita R., Nishii W., Muramatsu T., Ito H., Park SJ., Takahashi K., 2008, The effects of mutations in the carboxyl-terminal region on the catalytic activity of Escherichia coli signal peptidase I., J Biochem 143(2):237-42

 [11] Klenotic PA., Carlos JL., Samuelson JC., Schuenemann TA., Tschantz WR., Paetzel M., Strynadka NC., Dalbey RE., 2000, The role of the conserved box E residues in the active site of the Escherichia coli type I signal peptidase., J Biol Chem 275(9):6490-8

 [12] Moore KE., Miura S., 1987, A small hydrophobic domain anchors leader peptidase to the cytoplasmic membrane of Escherichia coli., J Biol Chem 262(18):8806-13

 [13] Musial-Siwek M., Kendall DA., Yeagle PL., 2008, Solution NMR of signal peptidase, a membrane protein., Biochim Biophys Acta 1778(4):937-44

 [14] Musik JE., Zalucki YM., Day CJ., Jennings MP., 2021, Expression of the Bacillus subtilis TasA signal peptide leads to cell death in Escherichia coli due to inefficient cleavage by LepB., Biochim Biophys Acta Biomembr 1863(12):183768

 [15] Ohno-Iwashita Y., Wolfe P., Ito K., Wickner W., 1984, Processing of preproteins by liposomes bearing leader peptidase., Biochemistry 23(25):6178-84

 [16] Sandhu H., Hedman R., Cymer F., Kudva R., Ismail N., von Heijne G., 2021, Cotranslational Translocation and Folding of a Periplasmic Protein Domain in Escherichia coli., J Mol Biol 433(15):167047

 [17] Stein RL., Barbosa MD., Bruckner R., 2000, Kinetic and mechanistic studies of signal peptidase I from Escherichia coli., Biochemistry 39(27):7973-83

 [18] Tschantz WR., Sung M., Delgado-Partin VM., Dalbey RE., 1993, A serine and a lysine residue implicated in the catalytic mechanism of the Escherichia coli leader peptidase., J Biol Chem 268(36):27349-54

 [19] Tuteja R., 2005, Type I signal peptidase: an overview., Arch Biochem Biophys 441(2):107-11

 [20] Wang Y., Bruckner R., Stein RL., 2004, Regulation of signal peptidase by phospholipids in membrane: characterization of phospholipid bilayer incorporated Escherichia coli signal peptidase., Biochemistry 43(1):265-70

 [21] 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.

 [22] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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