RegulonDB

Gene
Name:	lepB
Synonym(s):	ECK2566, EG10530, b2568, lep
Genome position(nucleotides):	2704335 <-- 2705309 Genome Browser
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

Gene

Name:

lepB

Synonym(s):

ECK2566, EG10530, b2568, lep

Genome position(nucleotides):

2704335 <-- 2705309 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.0

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

42 -> 43

269 -> 269

123 -> 123

154 -> 154

159 -> 159

Type

Positions

Sequence

42 -> 43

269 -> 269

123 -> 123

154 -> 154

159 -> 159

177 -> 177

274 -> 274

281 -> 281

144 -> 144

146 -> 146

128 -> 128

130 -> 130

147 -> 147

4 -> 22

MFALILVIATLVTGILWCV

78 -> 78

276 -> 276

283 -> 283

59 -> 77

GWLETGASVFPVLAIVLIV

60 -> 302

WLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWM

125 -> 125

183 -> 183

91 -> 91

236 -> 236

62 -> 62

171 -> 171

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:0015643 - toxic substance binding
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

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_2858	2703503	reverse	nd	[RS-EPT-CBR]	[20]
promoter	TSS_2859	2704008	reverse	nd	[RS-EPT-CBR]	[20]
promoter	TSS_2860 (cluster)	2704016	reverse	nd	[RS-EPT-CBR]	[20]
promoter	TSS_2861	2704074	reverse	nd	[RS-EPT-CBR]	[20]
promoter	TSS_2862	2704076	reverse	nd	[RS-EPT-CBR]	[20]
promoter	TSS_2863	2704093	reverse	nd	[RS-EPT-CBR]	[20]
promoter	TSS_2864	2704101	reverse	nd	[RS-EPT-CBR]	[20]
promoter	TSS_2865 (cluster)	2704183	reverse	nd	[RS-EPT-CBR]	[20]
promoter	lepBp1	2705464	reverse	nd	[ICWHO]	[21]
promoter	TSS_2866	2706051	reverse	nd	[RS-EPT-CBR]	[20]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_2858

2703503

reverse

[RS-EPT-CBR]

[20]

promoter

TSS_2859

2704008

reverse

[RS-EPT-CBR]

[20]

promoter

TSS_2860 (cluster)

2704016

reverse

[RS-EPT-CBR]

[20]

promoter

TSS_2861

2704074

reverse

[RS-EPT-CBR]

[20]

promoter

TSS_2862

2704076

reverse

[RS-EPT-CBR]

[20]

promoter

TSS_2863

2704093

reverse

[RS-EPT-CBR]

[20]

promoter

TSS_2864

2704101

reverse

[RS-EPT-CBR]

[20]

promoter

TSS_2865 (cluster)

2704183

reverse

[RS-EPT-CBR]

[20]

promoter

lepBp1

2705464

reverse

[ICWHO]

[21]

promoter

TSS_2866

2706051

reverse

[RS-EPT-CBR]

[20]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Evidence

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

[ICWHO] 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] Ohno-Iwashita Y., Wolfe P., Ito K., Wickner W., 1984, Processing of preproteins by liposomes bearing leader peptidase., Biochemistry 23(25):6178-84
[15] 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
[16] Stein RL., Barbosa MD., Bruckner R., 2000, Kinetic and mechanistic studies of signal peptidase I from Escherichia coli., Biochemistry 39(27):7973-83
[17] 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
[18] Tuteja R., 2005, Type I signal peptidase: an overview., Arch Biochem Biophys 441(2):107-11
[19] 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
[20] 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.
[21] 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

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