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Escherichia coli K-12 substr. MG1655 Enzyme: outer membrane protease VII (outer membrane protein 3b)



Gene: ompT Accession Numbers: EG10673 (EcoCyc), b0565, ECK0557

Synonyms: omptin

Regulation Summary Diagram: ?

Summary:
OmpT is an outer membrane protease with specificity for paired basic residues [Sugimura88]; detailed studies on substrate specificity have been performed [Dekker01, Okuno02, McCarter04]. Cellular localization studies have shown that OmpT localizes to the cellular poles [Lai04a]. Targeting of OmpT to the Sec-translocase for transport across the inner membrane is SecB-dependent [Baars06]. In vitro studies have investigated the strategies used by a number of outer-membrane proteins, including OmpT, to efficiently fold into the membrane [Burgess08].

OmpT is active under extreme denaturing conditions and shows a preference for denatured substrates [White95a]. It is responsible for hydrolysis of the antimicrobial peptide protamine [Stumpe98] and is a virulence determinant in urinary tract infections [Kanamaru03].

OmpT has been shown to be responsible for cleavage of the endonuclease colicin E2 (ColE2), a bacteriocidal protein, and the associated cognate immunity protein (Im2) in the presence of BtuB. Specifically, OmpT cleaves the C-terminal DNase domain of ColE2 [Duche09].

Kinetic parameters of the purified protein have been determined [Kramer00].

Based on information from a crystal structure, a novel catalytic mechanism was suggested [VandeputteRutte01]. Site-directed mutagenesis studies had previously identified essential active site residues Ser99 and His212 [Kramer00a]; mutational studies of additional residues support a novel catalytic mechanism [Kramer01].

OmpT expression and activity increases in response to heat shock as well as overexpression of recombinant proteins [Gill00, Jurgen00, Gill00a]. Expression is regulated by the EvgA/EvgS two-component system [Eguchi04].

Citations: [Stathopoulos98, Kukkonen04]

Gene Citations: [Lundrigan84, Blattner97]

Locations: outer membrane

Map Position: [583,903 <- 584,856] (12.58 centisomes)
Length: 954 bp / 317 aa

Molecular Weight of Polypeptide: 35.562 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001931 , CGSC:4984 , EchoBASE:EB0667 , EcoGene:EG10673 , EcoliWiki:b0565 , ModBase:P09169 , OU-Microarray:b0565 , PortEco:ompT , PR:PRO_000023458 , Pride:P09169 , Protein Model Portal:P09169 , RefSeq:NP_415097 , RegulonDB:EG10673 , SMR:P09169 , String:511145.b0565 , UniProt:P09169

Relationship Links: InterPro:IN-FAMILY:IPR000036 , InterPro:IN-FAMILY:IPR020079 , InterPro:IN-FAMILY:IPR020080 , InterPro:IN-FAMILY:IPR023619 , PDB:Structure:1I78 , Pfam:IN-FAMILY:PF01278 , Prints:IN-FAMILY:PR00482 , Prosite:IN-FAMILY:PS00834 , Prosite:IN-FAMILY:PS00835

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Grodberg88, Kramer00]
Molecular Function: GO:0004175 - endopeptidase activity Inferred from experiment Inferred by computational analysis [GOA01a, Grodberg88]
GO:0004252 - serine-type endopeptidase activity Inferred from experiment [Kramer00a]
GO:0004190 - aspartic-type endopeptidase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0009279 - cell outer membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA01a, DiazMejia09, Han12, Zhang07, Molloy00, LopezCampistrou05, Grodberg88, Lai04a]
GO:0031230 - intrinsic component of cell outer membrane Inferred from experiment [Rupprecht83, Kramer00a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell structure membrane
extrachromosomal prophage genes and phage related functions
metabolism degradation of macromolecules proteins/peptides/glycopeptides

Essentiality data for ompT 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]

Credits:
Revised 25-May-2011 by Brito D


Enzymatic reaction of: protease

EC Number: 3.4.23.49

a protein + 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 Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

T(opt): 25 °C [BRENDA14, Ono07], 45 °C [BRENDA14, Mangel94]

pH(opt): 5 [BRENDA14, Mangel94], 6 [BRENDA14, Sugimura88], 6.5 [BRENDA14, Kramer00]


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 20
[Kramer00, Sugimura88, Grodberg88a, Molloy98, UniProt11]
.
Chain 21 -> 317
[UniProt09]
UniProt: Protease 7;
Transmembrane-Region 32 -> 41
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Transmembrane-Region 70 -> 78
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Transmembrane-Region 84 -> 92
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 103
[Kramer01, UniProt11]
Alternate sequence: D → A; UniProt: Loss of activity.
Active-Site 103
[UniProt10]
UniProt: Non-Experimental Qualifier: probable;
Mutagenesis-Variant 105
[Kramer01, UniProt11]
Alternate sequence: D → A; UniProt: Loss of activity.
Active-Site 105
[UniProt10]
UniProt: Non-Experimental Qualifier: probable;
Transmembrane-Region 131 -> 140
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Transmembrane-Region 146 -> 156
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Transmembrane-Region 198 -> 209
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Transmembrane-Region 212 -> 221
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 230
[Kramer01, UniProt11]
Alternate sequence: D → A; UniProt: Loss of activity.
Active-Site 230
[UniProt10]
UniProt: Non-Experimental Qualifier: probable;
Active-Site 232
[UniProt10]
UniProt: Non-Experimental Qualifier: probable;
Mutagenesis-Variant 236 -> 237
[Kramer00, UniProt11]
Alternate sequence: GK → KG; UniProt: 70% of wild-type enzymatic activity.
Mutagenesis-Variant 237
[Kramer00, UniProt11]
Alternate sequence: K → T; UniProt: 40% of wild-type enzymatic activity.
Mutagenesis-Variant 238
[UniProt10a]
Alternate sequence: R → L; UniProt: Loss of activity;
Transmembrane-Region 251 -> 261
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Transmembrane-Region 265 -> 274
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;
Transmembrane-Region 307 -> 316
[UniProt10]
UniProt: Beta stranded;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0565 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10673; confirmed by SwissProt match.


References

Baars06: Baars L, Ytterberg AJ, Drew D, Wagner S, Thilo C, van Wijk KJ, de Gier JW (2006). "Defining the role of the Escherichia coli chaperone SecB using comparative proteomics." J Biol Chem 281(15);10024-34. PMID: 16352602

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

Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Burgess08: Burgess NK, Dao TP, Stanley AM, Fleming KG (2008). "Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro." J Biol Chem 283(39);26748-58. PMID: 18641391

Dekker01: Dekker N, Cox RC, Kramer RA, Egmond MR (2001). "Substrate specificity of the integral membrane protease OmpT determined by spatially addressed peptide libraries." Biochemistry 40(6);1694-701. PMID: 11327829

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

Duche09: Duche D, Issouf M, Lloubes R (2009). "Immunity Protein Protects Colicin E2 from OmpT Protease." J Biochem 145(1);95-101. PMID: 18990718

Eguchi04: Eguchi Y, Okada T, Minagawa S, Oshima T, Mori H, Yamamoto K, Ishihama A, Utsumi R (2004). "Signal transduction cascade between EvgA/EvgS and PhoP/PhoQ two-component systems of Escherichia coli." J Bacteriol 186(10);3006-14. PMID: 15126461

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

Gill00: Gill RT, DeLisa MP, Shiloach M, Holoman TR, Bentley WE (2000). "OmpT expression and activity increase in response to recombinant chloramphenicol acetyltransferase overexpression and heat shock in E. coli." J Mol Microbiol Biotechnol 2(3);283-9. PMID: 10937437

Gill00a: Gill RT, Valdes JJ, Bentley WE (2000). "A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli." Metab Eng 2(3);178-89. PMID: 11056060

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

Grodberg88: Grodberg J, Dunn JJ (1988). "ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification." J Bacteriol 170(3);1245-53. PMID: 3277950

Grodberg88a: Grodberg J, Lundrigan MD, Toledo DL, Mangel WF, Dunn JJ (1988). "Complete nucleotide sequence and deduced amino acid sequence of the ompT gene of Escherichia coli K-12." Nucleic Acids Res 16(3);1209. PMID: 3278297

Han12: Han MJ, Lee SY, Hong SH (2012). "Comparative analysis of envelope proteomes in Escherichia coli B and K-12 strains." J Microbiol Biotechnol 22(4);470-8. PMID: 22534293

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

Jurgen00: Jurgen B, Lin HY, Riemschneider S, Scharf C, Neubauer P, Schmid R, Hecker M, Schweder T (2000). "Monitoring of genes that respond to overproduction of an insoluble recombinant protein in Escherichia coli glucose-limited fed-batch fermentations." Biotechnol Bioeng 70(2);217-24. PMID: 10972933

Kanamaru03: Kanamaru S, Kurazono H, Ishitoya S, Terai A, Habuchi T, Nakano M, Ogawa O, Yamamoto S (2003). "Distribution and genetic association of putative uropathogenic virulence factors iroN, iha, kpsMT, ompT and usp in Escherichia coli isolated from urinary tract infections in Japan." J Urol 170(6 Pt 1);2490-3. PMID: 14634457

Kramer00: Kramer RA, Zandwijken D, Egmond MR, Dekker N (2000). "In vitro folding, purification and characterization of Escherichia coli outer membrane protease ompT." Eur J Biochem 267(3);885-93. PMID: 10651827

Kramer00a: Kramer RA, Dekker N, Egmond MR (2000). "Identification of active site serine and histidine residues in Escherichia coli outer membrane protease OmpT." FEBS Lett 468(2-3);220-4. PMID: 10692590

Kramer01: Kramer RA, Vandeputte-Rutten L, de Roon GJ, Gros P, Dekker N, Egmond MR (2001). "Identification of essential acidic residues of outer membrane protease OmpT supports a novel active site." FEBS Lett 505(3);426-30. PMID: 11576541

Kukkonen04: Kukkonen M, Korhonen TK (2004). "The omptin family of enterobacterial surface proteases/adhesins: from housekeeping in Escherichia coli to systemic spread of Yersinia pestis." Int J Med Microbiol 294(1);7-14. PMID: 15293449

Lai04a: Lai EM, Nair U, Phadke ND, Maddock JR (2004). "Proteomic screening and identification of differentially distributed membrane proteins in Escherichia coli." Mol Microbiol 52(4);1029-44. PMID: 15130122

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

Lundrigan84: Lundrigan MD, Earhart CF (1984). "Gene envY of Escherichia coli K-12 affects thermoregulation of major porin expression." J Bacteriol 1984;157(1);262-8. PMID: 6317653

Mangel94: Mangel WF, Toledo DL, Brown MT, Worzalla K, Lee M, Dunn JJ (1994). "Omptin: an Escherichia coli outer membrane proteinase that activates plasminogen." Methods Enzymol 244;384-99. PMID: 7845221

McCarter04: McCarter JD, Stephens D, Shoemaker K, Rosenberg S, Kirsch JF, Georgiou G (2004). "Substrate specificity of the Escherichia coli outer membrane protease OmpT." J Bacteriol 186(17);5919-25. PMID: 15317797

Molloy00: Molloy MP, Herbert BR, Slade MB, Rabilloud T, Nouwens AS, Williams KL, Gooley AA (2000). "Proteomic analysis of the Escherichia coli outer membrane." Eur J Biochem 267(10);2871-81. PMID: 10806384

Molloy98: Molloy MP, Herbert BR, Walsh BJ, Tyler MI, Traini M, Sanchez JC, Hochstrasser DF, Williams KL, Gooley AA (1998). "Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis." Electrophoresis 19(5);837-44. PMID: 9629924

Okuno02: Okuno K, Yabuta M, Kawanishi K, Ohsuye K, Ooi T, Kinoshita S (2002). "Substrate specificity at the P1' site of Escherichia coli OmpT under denaturing conditions." Biosci Biotechnol Biochem 66(1);127-34. PMID: 11866094

Ono07: Ono B, Kimiduka H, Kubota M, Okuno K, Yabuta M (2007). "Role of the ompT mutation in stimulated decrease in colony-forming ability due to intracellular protein aggregate formation in Escherichia coli strain BL21." Biosci Biotechnol Biochem 71(2);504-12. PMID: 17284844

Rupprecht83: Rupprecht KR, Gordon G, Lundrigan M, Gayda RC, Markovitz A, Earhart C (1983). "omp T: Escherichia coli K-12 structural gene for protein a (3b)." J Bacteriol 153(2);1104-6. PMID: 6337119

Stathopoulos98: Stathopoulos C (1998). "Structural features, physiological roles, and biotechnological applications of the membrane proteases of the OmpT bacterial endopeptidase family: a micro-review." Membr Cell Biol 12(1);1-8. PMID: 9829254

Stumpe98: Stumpe S, Schmid R, Stephens DL, Georgiou G, Bakker EP (1998). "Identification of OmpT as the protease that hydrolyzes the antimicrobial peptide protamine before it enters growing cells of Escherichia coli." J Bacteriol 180(15);4002-6. PMID: 9683502

Sugimura88: Sugimura K, Nishihara T (1988). "Purification, characterization, and primary structure of Escherichia coli protease VII with specificity for paired basic residues: identity of protease VII and OmpT." J Bacteriol 170(12);5625-32. PMID: 3056908

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

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.

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

VandeputteRutte01: Vandeputte-Rutten L, Kramer RA, Kroon J, Dekker N, Egmond MR, Gros P (2001). "Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site." EMBO J 20(18);5033-9. PMID: 11566868

White95a: White CB, Chen Q, Kenyon GL, Babbitt PC (1995). "A novel activity of OmpT. Proteolysis under extreme denaturing conditions." J Biol Chem 270(22);12990-4. PMID: 7768890

Zhang07: 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

Other References Related to Gene Regulation

Guillier08: Guillier M, Gottesman S (2008). "The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator." Nucleic Acids Res 36(21):6781-94. PMID: 18953042

Minagawa03: Minagawa S, Ogasawara H, Kato A, Yamamoto K, Eguchi Y, Oshima T, Mori H, Ishihama A, Utsumi R (2003). "Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli." J Bacteriol 185(13);3696-702. PMID: 12813061

Zwir05: Zwir I, Shin D, Kato A, Nishino K, Latifi T, Solomon F, Hare JM, Huang H, Groisman EA (2005). "Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica." Proc Natl Acad Sci U S A 102(8);2862-7. PMID: 15703297


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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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