Escherichia coli K-12 substr. MG1655 Enzyme: protease IV, a signal peptide peptidase

Gene: sppA Accession Numbers: EG10968 (EcoCyc), b1766, ECK1764

Regulation Summary Diagram: ?

Regulation summary diagram for sppA

Subunit composition of protease IV, a signal peptide peptidase = [SppA]4
         protease IV = SppA

Protease IV is an endopeptidase that degrades cleaved lipoprotein signal peptide [Ichihara84]. It may not be the only protease carrying out this function, as signal peptide is still degraded, albeit slowly, in its absence [Suzuki87]. Protease IV functions as a tetramer [Ichihara86] with a novel bowl shaped architecture [Kim08b]. Analysis of the peptide fragments generated from cleavage of prolipoprotein signal peptide by purified SppA suggests that it cleaves predominantly in the hydrophobic segment of the signal peptide [Novak88].

SppA has one transmembrane segment (spanning residues 29-45) and the carboxy-terminal domain is located in the periplasm [Wang08b].

Deletion of sppA did not affect degradation of the signal peptides of fusion proteins in vivo [Saito11].

Citations: [Regnier81, Regnier81a, Pacaud82, Hussain82]

Locations: inner membrane

Map Position: [1,846,861 -> 1,848,717] (39.81 centisomes, 143°)
Length: 1857 bp / 618 aa

Molecular Weight of Polypeptide: 67.219 kD (from nucleotide sequence), 67.0 kD (experimental)

Unification Links: ASAP:ABE-0005880 , CGSC:13763 , EchoBASE:EB0961 , EcoGene:EG10968 , EcoliWiki:b1766 , EcoO157Cyc:SPPA-MONOMER , ModBase:P08395 , OU-Microarray:b1766 , PortEco:sppA , PR:PRO_000023978 , Pride:P08395 , Protein Model Portal:P08395 , RefSeq:NP_416280 , RegulonDB:EG10968 , SMR:P08395 , String:511145.b1766 , UniProt:P08395

Relationship Links: InterPro:IN-FAMILY:IPR002142 , InterPro:IN-FAMILY:IPR004634 , InterPro:IN-FAMILY:IPR004635 , InterPro:IN-FAMILY:IPR029045 , PDB:Structure:3BEZ , PDB:Structure:3BF0 , Pfam:IN-FAMILY:PF01343

In Paralogous Gene Group: 270 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006465 - signal peptide processing Inferred from experiment Inferred by computational analysis [GOA01a, Suzuki87]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004175 - endopeptidase activity Inferred from experiment [Ichihara86]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008236 - serine-type peptidase activity Inferred by computational analysis [UniProtGOA11a]
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, Zhang07a, LopezCampistrou05, Ichihara86]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Ichihara86]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lasserre06]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: information transfer protein related turnover, degradation
metabolism degradation of macromolecules proteins/peptides/glycopeptides

Essentiality data for sppA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 23-Aug-2011 by Mackie A , Macquarie University

Enzymatic reaction of: signal peptide peptidase

EC Number: 3.4.21.-

a cleaved lipoprotein signal peptide + H2O <=> n a peptide

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 physiologically favored in the direction shown.

Sequence Features

Protein sequence of protease IV with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 25 -> 45
UniProt: Helical.
Transmembrane-Region 29 -> 45
[UniProt10, Wang08b]
UniProt: Helical;
Extrinsic-Sequence-Variant 151
UniProt: In strain: ECOR 49 and ECOR 50..
Extrinsic-Sequence-Variant 186
UniProt: In strain: ECOR 16..
Mutagenesis-Variant 209
[Wang08b, UniProt11]
UniProt: Loss of activity.
Active-Site 209
UniProt: Proton acceptor; Non-Experimental Qualifier: probable;
Extrinsic-Sequence-Variant 252
E → H: In strain: ECOR 16..
E → Q: In strain: ECOR 38, ECOR 39, ECOR 40, ECOR 50, ECOR 65 and ECOR 68..
E → K: In strain: ECOR 49..
Extrinsic-Sequence-Variant 294
UniProt: In strain: ECOR 38, ECOR 39, ECOR 40, ECOR 49, ECOR 50 and ECOR 65..
Mutagenesis-Variant 366
[Wang08b, UniProt11]
UniProt: Reduced activity.
Sequence-Conflict 378
[Ichihara86, Guttman94, UniProt10]
UniProt: (in Ref. 1; AAA24648 and 5; AAA57009);
Active-Site 409
UniProt: Nucleophile.
Mutagenesis-Variant 409
[Wang08b, UniProt11]
UniProt: Loss of activity.
Mutagenesis-Variant 410
[Wang08b, UniProt11]
UniProt: Reduced activity.
Mutagenesis-Variant 412
[Wang08b, UniProt11]
UniProt: No effect on activity.
Mutagenesis-Variant 510
[Wang08b, UniProt11]
UniProt: Reduced activity.
Mutagenesis-Variant 524
[Wang08b, UniProt11]
UniProt: Increased activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b1766 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10968; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Guttman94: Guttman DS, Dykhuizen DE (1994). "Clonal divergence in Escherichia coli as a result of recombination, not mutation." Science 266(5189);1380-3. PMID: 7973728

Hussain82: Hussain M, Ichihara S, Mizushima S (1982). "Mechanism of signal peptide cleavage in the biosynthesis of the major lipoprotein of the Escherichia coli outer membrane." J Biol Chem 257(9);5177-82. PMID: 7040395

Ichihara84: Ichihara S, Beppu N, Mizushima S (1984). "Protease IV, a cytoplasmic membrane protein of Escherichia coli, has signal peptide peptidase activity." J Biol Chem 259(15);9853-7. PMID: 6378913

Ichihara86: Ichihara S, Suzuki T, Suzuki M, Mizushima S (1986). "Molecular cloning and sequencing of the sppA gene and characterization of the encoded protease IV, a signal peptide peptidase, of Escherichia coli." J Biol Chem 261(20);9405-11. PMID: 3522590

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kim08b: Kim AC, Oliver DC, Paetzel M (2008). "Crystal structure of a bacterial signal Peptide peptidase." J Mol Biol 376(2);352-66. PMID: 18164727

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Novak88: Novak P, Dev IK (1988). "Degradation of a signal peptide by protease IV and oligopeptidase A." J Bacteriol 170(11);5067-75. PMID: 3053642

Pacaud82: Pacaud M (1982). "Purification and characterization of two novel proteolytic enzymes in membranes of Escherichia coli. Protease IV and protease V." J Biol Chem 257(8);4333-9. PMID: 7040383

Regnier81: Regnier P (1981). "Identification of protease IV of E, coli." Biochem Biophys Res Commun 99(3);844-54. PMID: 7018496

Regnier81a: Regnier P (1981). "The purification of protease IV of E. coli and the demonstration that it is an endoproteolytic enzyme." Biochem Biophys Res Commun 99(4);1369-76. PMID: 7020700

Saito11: Saito A, Hizukuri Y, Matsuo E, Chiba S, Mori H, Nishimura O, Ito K, Akiyama Y (2011). "Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria." Proc Natl Acad Sci U S A 108(33);13740-5. PMID: 21810987

Suzuki87: Suzuki T, Itoh A, Ichihara S, Mizushima S (1987). "Characterization of the sppA gene coding for protease IV, a signal peptide peptidase of Escherichia coli." J Bacteriol 169(6);2523-8. PMID: 3294796

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wang08b: Wang P, Shim E, Cravatt B, Jacobsen R, Schoeniger J, Kim AC, Paetzel M, Dalbey RE (2008). "Escherichia coli signal peptide peptidase A is a serine-lysine protease with a lysine recruited to the nonconserved amino-terminal domain in the S49 protease family." Biochemistry 47(24);6361-9. PMID: 18476724

Zhang07a: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

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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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