Escherichia coli K-12 substr. MG1655 Enzyme: oligopeptidase B

Gene: ptrB Accession Numbers: EG11004 (EcoCyc), b1845, ECK1846

Synonyms: tlp, protease II

Regulation Summary Diagram: ?

Regulation summary diagram for ptrB

Oligopeptidase B, originally called protease II, is a serine protease that hydrolyzes peptide bonds following arginines and lysines [Kanatani91]. The enzyme is very efficient at cleaving after paired basic amino acid residues such as Arg-Arg [Polgar97]. Its specificity for artificial peptide substrates has been compared with oligopeptidase A [Yan06] and oligopeptidases from other organisms [Mohamed12].

The enzyme belongs to the prolyl oligopeptidase family of serine peptidases [Rawlings91, Polgar97].

Citations: [Kanatani92, Tsuru94, Polgar98, Tsuji06]

Locations: cytosol

Map Position: [1,924,803 <- 1,926,863] (41.49 centisomes, 149°)
Length: 2061 bp / 686 aa

Molecular Weight of Polypeptide: 79.49 kD (from nucleotide sequence), 80.0 kD (experimental) [Kanatani91 ]

Unification Links: ASAP:ABE-0006133 , CGSC:32339 , EchoBASE:EB0997 , EcoGene:EG11004 , EcoliWiki:b1845 , EcoO157Cyc:PTRB-MONOMER , ModBase:P24555 , OU-Microarray:b1845 , PortEco:ptrB , PR:PRO_000023630 , Protein Model Portal:P24555 , RefSeq:NP_416359 , RegulonDB:EG11004 , SMR:P24555 , String:511145.b1845 , UniProt:P24555

Relationship Links: InterPro:IN-FAMILY:IPR001375 , InterPro:IN-FAMILY:IPR002470 , InterPro:IN-FAMILY:IPR002471 , InterPro:IN-FAMILY:IPR023302 , InterPro:IN-FAMILY:IPR029058 , Panther:IN-FAMILY:PTHR11757 , Pfam:IN-FAMILY:PF00326 , Pfam:IN-FAMILY:PF02897 , Prints:IN-FAMILY:PR00862 , Prosite:IN-FAMILY:PS00708

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a, GOA01]
Molecular Function: GO:0004252 - serine-type endopeptidase activity Inferred from experiment Inferred by computational analysis [GOA01, Kanatani91]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0008236 - serine-type peptidase activity Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0070008 - serine-type exopeptidase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Pacaud75]

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

Essentiality data for ptrB 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 ? 10-Jan-2013 by Keseler I , SRI International

Enzymatic reaction of: oligopeptidase

Synonyms: protease

EC Number:

an oligopeptide + H2O <=> a peptide + 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.

Protease II was initially purified from E. coli B [Pacaud75, Pacaud76, Pacaud78].

Inhibitors (Competitive): protamine (Kic = 0.011µM) [Tsuji06]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
an oligopeptide

T(opt): 25 °C [Polgar99, BRENDA14, Juhasz02], 39 °C [BRENDA14, Polgar99]

pH(opt): 7.5 [BRENDA14, Pacaud75], 7.6 [BRENDA14, Pacaud75], 8 [Kanatani91]

Sequence Features

Protein sequence of oligopeptidase B with features indicated

Feature Class Location Citations Comment
Active-Site 532
[Kanatani91, UniProt11a]
UniProt: Charge relay system.
Active-Site 617
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity;
Active-Site 652
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 682 -> 686
[Kanatani91, UniProt10a]
UniProt: (in Ref. 1; AA sequence);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b1845 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11004; 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

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

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Juhasz02: Juhasz T, Szeltner Z, Renner V, Polgar L (2002). "Role of the oxyanion binding site and subsites S1 and S2 in the catalysis of oligopeptidase B, a novel target for antimicrobial chemotherapy." Biochemistry 41(12);4096-106. PMID: 11900553

Kanatani91: Kanatani A, Masuda T, Shimoda T, Misoka F, Lin XS, Yoshimoto T, Tsuru D (1991). "Protease II from Escherichia coli: sequencing and expression of the enzyme gene and characterization of the expressed enzyme." J Biochem 110(3);315-20. PMID: 1769955

Kanatani92: Kanatani A, Yoshimoto T, Nagai H, Ito K, Tsuru D (1992). "Location of the protease II gene (ptrB) on the physical map of the Escherichia coli chromosome." J Bacteriol 174(23);7881. PMID: 1447164

Mohamed12: Mohamed Mustafa MS, Nakajima Y, Oyama H, Iwata N, Ito K (2012). "Assessment of substrate inhibition of bacterial oligopeptidase B." Biol Pharm Bull 35(11);2010-6. PMID: 23123472

Pacaud75: Pacaud M, Richaud C (1975). "Protease II from Escherichia coli. Purification and characterization." J Biol Chem 250(19);7771-9. PMID: 240839

Pacaud76: Pacaud M (1976). "Purification of protease II from Escherichia coli by affinity chromatography and separation of two enzyme species from cells harvested at late log phase." Eur J Biochem 64(1);199-204. PMID: 776612

Pacaud78: Pacaud M (1978). "Protease II from Escherichia coli. Substrate specificity and kinetic properties." Eur J Biochem 82(2);439-51. PMID: 342237

Polgar97: Polgar L (1997). "A potential processing enzyme in prokaryotes: oligopeptidase B, a new type of serine peptidase." Proteins 28(3);375-9. PMID: 9223183

Polgar98: Polgar L, Felfoldi F (1998). "Oligopeptidase B: cloning and probing stability under nonequilibrium conditions." Proteins 30(4);424-34. PMID: 9533626

Polgar99: Polgar L (1999). "Oligopeptidase B: a new type of serine peptidase with a unique substrate-dependent temperature sensitivity." Biochemistry 38(47);15548-55. PMID: 10569938

Rawlings91: Rawlings ND, Polgar L, Barrett AJ (1991). "A new family of serine-type peptidases related to prolyl oligopeptidase." Biochem J 279 ( Pt 3);907-8. PMID: 1953688

Strongin79: Strongin AY, Gorodetsky DI, Stepanov VM (1979). "The study of Escherichia coli proteases. Intracellular serine protease of E. coli-an analogue of bacillus proteases." J Gen Microbiol 110(2);443-51. PMID: 374683

Tsuji06: Tsuji A, Yoshimoto T, Yuasa K, Matsuda Y (2006). "Protamine: a unique and potent inhibitor of oligopeptidase B." J Pept Sci 12(1);65-71. PMID: 15948139

Tsuru94: Tsuru D, Yoshimoto T (1994). "Oligopeptidase B: protease II from Escherichia coli." Methods Enzymol 244;201-15. PMID: 7845209

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

Yan06: Yan JB, Wang GQ, Du P, Zhu DX, Wang MW, Jiang XY (2006). "High-level expression and purification of Escherichia coli oligopeptidase B." Protein Expr Purif 47(2);645-50. PMID: 16515865

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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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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