Escherichia coli K-12 substr. MG1655 Enzyme: protease III

Gene: ptrA Accession Numbers: EG10786 (EcoCyc), b2821, ECK2817

Synonyms: ptr, Pitrilysin, Protease pi

Regulation Summary Diagram: ?

Regulation summary diagram for ptrA

Protease III is a periplasmic protein that rapidly degrades small proteins and peptides in vitro [Swamy82, Cheng79, Cornista04, Anastasi93]. Protease III is partially responsible for degrading A-β-lactamase as well as misfolded MalE31 [Baneyx91, Betton98].

Protease III is a zinc metalloendopeptidase with a nontraditional zinc-binding motif, featuring the consensus sequence HXXEH rather than the more traditional HEXXH [Ding92, Becker92]. In addition to the two histidines in the zinc-binding motif, glutamate162 is also required for zinc coordination [Becker93].

A 50 kDa polypeptide with no apparent protease function derived from the N-terminal end of protease III can be found in the periplasm under some circumstances [Dykstra85].

Citations: [Anastasi95, Becker95a]

Gene Citations: [ClaverieMartin87]

Locations: periplasmic space, cytosol

Map Position: [2,954,018 <- 2,956,906] (63.67 centisomes, 229°)
Length: 2889 bp / 962 aa

Molecular Weight of Polypeptide: 107.71 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009252 , CGSC:351 , EchoBASE:EB0779 , EcoGene:EG10786 , EcoliWiki:b2821 , EcoO157Cyc:PTR-MONOMER , ModBase:P05458 , OU-Microarray:b2821 , PortEco:ptrA , PR:PRO_000023629 , Pride:P05458 , Protein Model Portal:P05458 , RefSeq:NP_417298 , RegulonDB:EG10786 , SMR:P05458 , String:511145.b2821 , UniProt:P05458

Relationship Links: InterPro:IN-FAMILY:IPR001431 , InterPro:IN-FAMILY:IPR007863 , InterPro:IN-FAMILY:IPR011237 , InterPro:IN-FAMILY:IPR011249 , InterPro:IN-FAMILY:IPR011765 , PDB:Structure:1Q2L , Pfam:IN-FAMILY:PF00675 , Pfam:IN-FAMILY:PF05193 , Prosite:IN-FAMILY:PS00143

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for ptrA

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01, Cheng79, Swamy82]
Molecular Function: GO:0004222 - metalloendopeptidase activity Inferred from experiment Inferred by computational analysis [GOA01, Cheng79]
GO:0008237 - metallopeptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Ding92]
GO:0008270 - zinc ion binding Inferred from experiment [Ding92]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Cheng79]
GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, Han14, LopezCampistrou05, Swamy82]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

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

Essentiality data for ptrA 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]

Revised 25-May-2011 by Brito D

Enzymatic reaction of: protease

EC Number:

a protein + 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.

T(opt): 45 °C [BRENDA14, Fricke95a]

pH(opt): 7.5 [BRENDA14, Anastasi95]

Sequence Features

Protein sequence of protease III with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
Chain 24 -> 962
UniProt: Protease 3;
Mutagenesis-Variant 88
UniProt: Loss of activity and of Zn-binding.
Metal-Binding-Site 88
[Becker92, UniProt11]
UniProt: Zinc.
Mutagenesis-Variant 91
UniProt: Loss of activity.
Active-Site 91
[Becker93, Becker92, UniProt11]
UniProt: Proton acceptor.
Mutagenesis-Variant 92
UniProt: Loss of activity and of Zn-binding.
Metal-Binding-Site 92
[Becker92, UniProt11]
UniProt: Zinc.
Mutagenesis-Variant 162
UniProt: 20% loss of activity.
Mutagenesis-Variant 169
UniProt: Loss of activity and of Zn-binding.
Metal-Binding-Site 169
UniProt: Zinc.
Mutagenesis-Variant 204
UniProt: No loss of activity.
Sequence-Conflict 277 -> 284
[ClaverieMartin87, UniProt10a]
UniProt: (in Ref. 5; AAA24436);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2821 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10786; confirmed by SwissProt match.


Anastasi93: Anastasi A, Knight CG, Barrett AJ (1993). "Characterization of the bacterial metalloendopeptidase pitrilysin by use of a continuous fluorescence assay." Biochem J 290 ( Pt 2);601-7. PMID: 7680857

Anastasi95: Anastasi A, Barrett AJ (1995). "Pitrilysin." Methods Enzymol 248;684-92. PMID: 7674955

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

Baneyx91: Baneyx F, Georgiou G (1991). "Construction and characterization of Escherichia coli strains deficient in multiple secreted proteases: protease III degrades high-molecular-weight substrates in vivo." J Bacteriol 173(8);2696-703. PMID: 2013581

Becker92: Becker AB, Roth RA (1992). "An unusual active site identified in a family of zinc metalloendopeptidases." Proc Natl Acad Sci U S A 89(9);3835-9. PMID: 1570301

Becker93: Becker AB, Roth RA (1993). "Identification of glutamate-169 as the third zinc-binding residue in proteinase III, a member of the family of insulin-degrading enzymes." Biochem J 292 ( Pt 1);137-42. PMID: 8099278

Becker95a: Becker AB, Roth RA (1995). "Insulysin and pitrilysin: insulin-degrading enzymes of mammals and bacteria." Methods Enzymol 248;693-703. PMID: 7674956

Betton98: Betton JM, Sassoon N, Hofnung M, Laurent M (1998). "Degradation versus aggregation of misfolded maltose-binding protein in the periplasm of Escherichia coli." J Biol Chem 273(15);8897-902. PMID: 9535871

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

Cheng79: Cheng YS, Zipser D (1979). "Purification and characterization of protease III from Escherichia coli." J Biol Chem 254(11);4698-706. PMID: 374413

ClaverieMartin87: Claverie-Martin F, Diaz-Torres MR, Kushner SR (1987). "Analysis of the regulatory region of the protease III (ptr) gene of Escherichia coli K-12." Gene 1987;54(2-3);185-95. PMID: 3308636

Cornista04: Cornista J, Ikeuchi S, Haruki M, Kohara A, Takano K, Morikawa M, Kanaya S (2004). "Cleavage of various peptides with pitrilysin from Escherichia coli: kinetic analyses using beta-endorphin and its derivatives." Biosci Biotechnol Biochem 68(10);2128-37. PMID: 15502359

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

Ding92: Ding L, Becker AB, Suzuki A, Roth RA (1992). "Comparison of the enzymatic and biochemical properties of human insulin-degrading enzyme and Escherichia coli protease III." J Biol Chem 267(4);2414-20. PMID: 1733942

Dykstra85: Dykstra CC, Kushner SR (1985). "Physical characterization of the cloned protease III gene from Escherichia coli K-12." J Bacteriol 163(3);1055-9. PMID: 2993229

Fricke95a: Fricke B, Betz R, Friebe S (1995). "A periplasmic insulin-cleaving proteinase (ICP) from Acinetobacter calcoaceticus sharing properties with protease III from Escherichia coli and IDE from eucaryotes." J Basic Microbiol 35(1);21-31. PMID: 7738784

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."

Han14: Han MJ, Kim JY, Kim JA (2014). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng 117(4);437-42. PMID: 24140104

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

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

Swamy82: Swamy KH, Goldberg AL (1982). "Subcellular distribution of various proteases in Escherichia coli." J Bacteriol 149(3);1027-33. PMID: 7037737

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

Other References Related to Gene Regulation

Wade05: Wade JT, Reppas NB, Church GM, Struhl K (2005). "Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites." Genes Dev 19(21);2619-30. PMID: 16264194

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Sun Oct 4, 2015, biocyc13.