Escherichia coli K-12 substr. MG1655 Enzyme: leader peptidase (signal peptidase I)

Gene: lepB Accession Numbers: EG10530 (EcoCyc), b2568, ECK2566

Synonyms: lep, LP1, SPase I

Regulation Summary Diagram: ?

Regulation summary diagram for lepB

Signal peptidase catalyzes the cleavage of the amino-terminal leader or signal peptide from membrane-tethered secretory pre-proteins [Dalbey85, Chatterjee95]. The action of signal peptidase releases the mature secretory protein into the periplasm and retains the signal peptide in the membrane where it is further degraded by the inner membrane protease RseP. Signal peptidase cleaves pre-proteins translocated by both the general Sec-system and the twin-arginine translocation (Tat) system [Luke09]. Signal peptidase also cleaves the signal peptide from bacteriophage M13 procoat protein [Chang78, Zwizinski80, Date81]. Signal peptidase is required for import of the bacterial toxin, colicin D [deZamaroczy01]

Signal peptidase has two N-terminal transmembrane segments separated by a small cytoplasmic domain and a large C-terminal catalytic domain that is located in the periplasm. The second transmembrane segment is believed to function as a non-cleavable signal sequence [Moore87, Dalbey87, Dalbey87a, San89, Bilgin90]. A soluble form of leader peptidase which lacks residues 2-76 is catalytically active in vitro [Kuo93, Tschantz95, Paetzel02] and has been crystallised on its own and in complex with inhibitors [Paetzel95, Paetzel98, Paetzel02, Paetzel04, Luo09, Liu11]. The structure reveals a large hydrophobic region that extends across the active site and may be embedded in the outer leaflet of the inner membrane thus creating a 'pocket' which optimises contact with signal peptides exposed on the periplasmic surface of the inner membrane. LepB catalysis may utilise a Ser/Lys/Ser triad mechanism (reviewed in [Paetzel13].

E. coli LepB functions as a monomer and there are approximately 1000 molecules of LepB in each cell during exponential growth [vanKlompenburg]. lepB is essential [Date83, Dalbey85].

Purified LepB undergoes autocatalytic cleavage at the A38QA / A41 site which is protected in vivo by its cytoplasmic location [Talarico91].

Signal peptides in gram-negative bacteria have an average length of 25 residues and approximately 10% of genes in E. coli are thought to contain signal peptides ([Paetzel13] and references therein). The substrate sequence requirements of signal peptidase have been investigated [Dev90, Shen91, Karamyshev98, Pausova90] - they include conformation to the '-3,-1 rule' [vonHeijne83, Perlman83] which dictates a preference for small residues at the -3 and -1 amino acid positions relative to the cleavage site.

Signal peptidase is considered to be a valuable target in the development of novel anti-microbial drugs (reviewed in [Smitha11].

lep: leader peptidase

Reviews: [Dalbey91, Tschantz94, Gennity90, Paetzel13]
Comments: [vonHeijne98]

Citations: [Inada89, Tschantz93, Stein00, Karla05, Wang04, Auclair12, Tuteja05, Kim08a, Kim04c, Klenotic00, MusialSiwek08, Carlos00, Fikes90, Choo08, OhnoIwashita84]

Gene Citations: [March85]

Locations: inner membrane

Map Position: [2,702,357 <- 2,703,331] (58.24 centisomes, 210°)
Length: 975 bp / 324 aa

Molecular Weight of Polypeptide: 35.96 kD (from nucleotide sequence), 37 kD (experimental) [Wolfe82 ]

Unification Links: ASAP:ABE-0008450 , CGSC:573 , EchoBASE:EB0525 , EcoGene:EG10530 , EcoliWiki:b2568 , ModBase:P00803 , OU-Microarray:b2568 , PortEco:lepB , PR:PRO_000023080 , Pride:P00803 , Protein Model Portal:P00803 , RefSeq:NP_417063 , RegulonDB:EG10530 , SMR:P00803 , String:511145.b2568 , UniProt:P00803

Relationship Links: InterPro:IN-FAMILY:IPR000223 , InterPro:IN-FAMILY:IPR015927 , InterPro:IN-FAMILY:IPR019533 , InterPro:IN-FAMILY:IPR019756 , InterPro:IN-FAMILY:IPR019757 , InterPro:IN-FAMILY:IPR019758 , InterPro:IN-FAMILY:IPR019759 , InterPro:IN-FAMILY:IPR019766 , InterPro:IN-FAMILY:IPR028360 , Panther:IN-FAMILY:PTHR12383 , PDB:Structure:1B12 , PDB:Structure:1KN9 , PDB:Structure:1T7D , PDB:Structure:3IIQ , PDB:Structure:3S04 , Pfam:IN-FAMILY:PF00717 , Pfam:IN-FAMILY:PF10502 , Prints:IN-FAMILY:PR00727 , Prosite:IN-FAMILY:PS00501 , Prosite:IN-FAMILY:PS00760 , Prosite:IN-FAMILY:PS00761

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006465 - signal peptide processing Inferred from experiment [Chatterjee95, Zwizinski80, Dalbey85]
GO:0006508 - proteolysis Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Kim04c, Stein00]
GO:0016485 - protein processing Inferred from experiment [Karla05, deZamaroczy01]
Molecular Function: GO:0004175 - endopeptidase activity Inferred from experiment [Chatterjee95, Zwizinski80, Dalbey85]
GO:0004252 - serine-type endopeptidase activity Inferred from experiment [Sung92]
GO:0008233 - peptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Karla05, Kim04c]
GO:0015643 - toxic substance binding Inferred from experiment [deZamaroczy01]
GO:0008236 - serine-type peptidase activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Zhang07, Daley05, Stein00, Chang78]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Wolfe83]
GO:0016021 - integral component of membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Stein00]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structure membrane
information transfer protein related export, signal peptide cleavage

Essentiality data for lepB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Last-Curated ? 27-Jan-2014 by Mackie A , Macquarie University

Enzymatic reaction of: leader peptidase

EC Number:

a peptide with a leader sequence + H2O <=> a peptide + a leader sequence

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is irreversible in the direction shown.

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
a peptide with a leader sequence

T(opt): 37 °C [BRENDA14, Tschantz94]

pH(opt): 8 [BRENDA14, Wolfe83a], 8.5 [BRENDA14, Gallagher01a], 10 [BRENDA14, Kim95b]

Sequence Features

Protein sequence of leader peptidase (signal peptidase I) with features indicated

Feature Class Location Citations Comment
Blocking-Modification 1
[Wolfe83, UniProt11]
UniProt: Blocked amino end (Met).
Transmembrane-Region 4 -> 22
UniProt: Helical;; Non-Experimental Qualifier: probable;
Sequence-Conflict 42 -> 43
[Nashimoto95, Wolfe83, UniProt10a]
UniProt: (in Ref. 1 and 2);
Transmembrane-Region 59 -> 77
UniProt: Helical;; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 62
UniProt: Indifferent.
Mutagenesis-Variant 78
R → E, L or N: Indifferent.
Mutagenesis-Variant 91
UniProt: Loss of activity.
Active-Site 91
Sequence-Conflict 123
[Nashimoto95, Wolfe83, UniProt10a]
UniProt: (in Ref. 1 and 2);
Mutagenesis-Variant 125
UniProt: Indifferent.
Mutagenesis-Variant 128
UniProt: Small effect.
Mutagenesis-Variant 130
UniProt: Indifferent.
Mutagenesis-Variant 144
UniProt: Indifferent.
Mutagenesis-Variant 146
K → D, G, M or S: Loss of activity.
Active-Site 146
Mutagenesis-Variant 147
UniProt: Small effect.
Mutagenesis-Variant 154
D → N: Indifferent.
D → A: Loss of activity.
Mutagenesis-Variant 159
UniProt: Small effect.
Mutagenesis-Variant 171
UniProt: Indifferent.
Disulfide-Bond-Site 171, 177
Mutagenesis-Variant 177
UniProt: Indifferent.
Sequence-Conflict 183
[Nashimoto95, Wolfe83, UniProt10a]
UniProt: (in Ref. 1 and 2);
Mutagenesis-Variant 236
UniProt: Indifferent.
Mutagenesis-Variant 269
UniProt: Indifferent.
Mutagenesis-Variant 274
UniProt: Indifferent.
Mutagenesis-Variant 276
UniProt: Small effect.
Mutagenesis-Variant 281
UniProt: Indifferent.
Mutagenesis-Variant 283
UniProt: Small effect.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2568 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10530; confirmed by SwissProt match.


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Bilgin90: Bilgin N, Lee JI, Zhu HY, Dalbey R, von Heijne G (1990). "Mapping of catalytically important domains in Escherichia coli leader peptidase." EMBO J 9(9);2717-22. PMID: 2202591

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

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Chang78: Chang CN, Blobel G, Model P (1978). "Detection of prokaryotic signal peptidase in an Escherichia coli membrane fraction: endoproteolytic cleavage of nascent f1 pre-coat protein." Proc Natl Acad Sci U S A 75(1);361-5. PMID: 343108

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Karla05: 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. PMID: 15598653

Kim04c: 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. PMID: 15195997

Kim08a: 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. PMID: 18032415

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Klenotic00: 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. PMID: 10692453

Kuo93: Kuo DW, Chan HK, Wilson CJ, Griffin PR, Williams H, Knight WB (1993). "Escherichia coli leader peptidase: production of an active form lacking a requirement for detergent and development of peptide substrates." Arch Biochem Biophys 303(2);274-80. PMID: 8512314

Liu11: Liu J, Luo C, Smith PA, Chin JK, Page MG, Paetzel M, Romesberg FE (2011). "Synthesis and characterization of the arylomycin lipoglycopeptide antibiotics and the crystallographic analysis of their complex with signal peptidase." J Am Chem Soc 133(44);17869-77. PMID: 21999324

Luke09: Luke I, Handford JI, Palmer T, Sargent F (2009). "Proteolytic processing of Escherichia coli twin-arginine signal peptides by LepB." Arch Microbiol 191(12);919-25. PMID: 19809807

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OhnoIwashita84: Ohno-Iwashita Y, Wolfe P, Ito K, Wickner W (1984). "Processing of preproteins by liposomes bearing leader peptidase." Biochemistry 23(25);6178-84. PMID: 6395892

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UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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Zwizinski80: Zwizinski C, Wickner W (1980). "Purification and characterization of leader (signal) peptidase from Escherichia coli." J Biol Chem 255(16);7973-7. PMID: 6995457

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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