Skip to main content

Advertisement

Log in

Bacterial β-peptidyl aminopeptidases: on the hydrolytic degradation of β-peptides

  • Mini-Review
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

The special chemical and biological features of β-peptides have been investigated intensively during recent years. Many studies emphasize the restricted biodegradability and the high metabolic stability of this class of compounds. β-Peptidyl aminopeptidases form the first family of enzymes that hydrolyze a variety of short β-peptides and β-amino-acid-containing peptides. All representatives of this family were isolated from Gram-negative bacteria. The substrate specificities of the peptidases vary greatly, but the enzymes have common structural properties, and a similar reaction mechanism can be expected. This review gives an overview on the β-peptidyl aminopeptidases with emphasis on their biochemical and structural properties. Their possible physiological function is discussed. Functionally and structurally related enzymes are compared to the β-peptidyl aminopeptidases.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Scheme 1

Similar content being viewed by others

References

  • Bompard-Gilles C, Villeret V, Fanuel L, Joris B, Frère JM, Van Beeumen J (1999) Crystallization and preliminary X-ray analysis of a new l-aminopeptidase-d-amidase/d-esterase activated by a Gly-Ser peptide bond hydrolysis. Acta Crystallogr D Biol Crystallogr 55(Pt 3):699–701

    CAS  PubMed  Google Scholar 

  • Bompard-Gilles C, Remaut H, Villeret V, Prange T, Fanuel L, Delmarcelle M, Joris B, Frère J, Van Beeumen J (2000a) Crystal structure of a d-aminopeptidase from Ochrobactrum anthropi, a new member of the ‘penicillin-recognizing enzyme’ family. Structure 8:971–980

    CAS  PubMed  Google Scholar 

  • Bompard-Gilles C, Villeret V, Davies GJ, Fanuel L, Joris B, Frère JM, Van Beeumen J (2000b) A new variant of the Ntn hydrolase fold revealed by the crystal structure of l-aminopeptidase d-ala-esterase/amidase from Ochrobactrum anthropi. Structure Fold Des 8:153–162

    CAS  PubMed  Google Scholar 

  • Bourne DG, Jones GJ, Blakeley RL, Jones A, Negri AP, Riddles P (1996) Enzymatic pathway for the bacterial degradation of the cyanobacterial cyclic peptide toxin microcystin LR. Appl Environ Microbiol 62:4086–4094

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bourne DG, Riddles P, Jones GJ, Smith W, Blakeley RL (2001) Characterisation of a gene cluster involved in bacterial degradation of the cyanobacterial toxin microcystin LR. Environ Toxicol 16:523–534

    CAS  PubMed  Google Scholar 

  • Brannigan JA, Dodson G, Duggleby HJ, Moody PC, Smith JL, Tomchick DR, Murzin AG (1995) A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature 378:416–419

    CAS  PubMed  Google Scholar 

  • Burley SK, David PR, Taylor A, Lipscomb WN (1990) Molecular structure of leucine aminopeptidase at 2.7-Å resolution. Proc Natl Acad Sci USA 87:6878–6882

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng H, Grishin NV (2005) DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain. Protein Sci 14:1902–1910

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chévrier B, Schalk C, D’Orchymont H, Rondeau JM, Moras D, Tarnus C (1994) Crystal structure of Aeromonas proteolytica aminopeptidase: a prototypical member of the co-catalytic zinc enzyme family. Structure 2:283–291

    PubMed  Google Scholar 

  • Christenson JC, Pavia AT, Seskin K, Brockmeyer D, Korgenski EK, Jenkins E, Pierce J, Daly JA (1997) Meningitis due to Ochrobactrum anthropi: an emerging nosocomial pathogen. A report of 3 cases. Pediatr Neurosurg 27:218–221

    CAS  PubMed  Google Scholar 

  • Delière E, Vu-Thien H, Lévy V, Barquins S, Schlegel L, Bouvet A (2000) Epidemiological investigation of Ochrobactrum anthropi strains isolated from a haematology unit. J Hosp Infect 44:173–178

    PubMed  Google Scholar 

  • Elkins JM, Kershaw NJ, Schofield CJ (2005) X-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster. Biochem J 385:565–573

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ezzedine H, Mourad M, Van Ossel C, Logghe C, Squifflet JP, Renault F, Wauters G, Gigi J, Wilmotte L, Haxhe JJ (1994) An outbreak of Ochrobactrum anthropi bacteraemia in five organ transplant patients. J Hosp Infect 27:35–42

    CAS  PubMed  Google Scholar 

  • Fanuel L, Goffin C, Cheggour A, Devreese B, Van Driessche G, Joris B, Van Beeumen J, Frère JM (1999a) The DmpA aminopeptidase from Ochrobactrum anthropi LMG7991 is the prototype of a new terminal nucleophile hydrolase family. Biochem J 341:147–155

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fanuel L, Thamm I, Kostanjevecki V, Samyn B, Joris B, Goffin C, Brannigan J, Van Beeumen J, Frère JM (1999b) Two new aminopeptidases from Ochrobactrum anthropi active on d-alanyl-p-nitroanilide. Cell Mol Life Sci 55:812–818

    CAS  PubMed  Google Scholar 

  • Frackenpohl J, Arvidsson PI, Schreiber JV, Seebach D (2001) The outstanding biological stability of β- and γ-peptides toward proteolytic enzymes: an in vitro investigation with fifteen peptidases. Chembiochem 2:445–455

    CAS  PubMed  Google Scholar 

  • Frère JM, van Beeumen J (2004) DmpA l-aminopeptidase d-Ala esterase/amidase of Ochrobactrum anthropi. In: Barrett AJ, Rawlings ND, Woessner R (eds) Handbook of proteolytic enzymes, 2nd edn. Elsevier Academic, Amsterdam, pp 2055–2057

    Google Scholar 

  • Geueke B, Namoto K, Seebach D, Kohler HPE (2005) A novel β-peptidyl aminopeptidase (BapA) from strain 3-2W4 cleaves peptide bonds of synthetic β-tri-and β-dipeptides. J Bacteriol 187:5910–5917

    CAS  PubMed  PubMed Central  Google Scholar 

  • Geueke B, Heck T, Limbach M, Seebach D, Kohler HPE (2006) Bacterial β-peptidyl aminopeptidases with unique substrate specificities for β- and mixed β/α-oligopeptides. FEBS J 273:5261–5272

    CAS  PubMed  Google Scholar 

  • Geueke B, Busse HJ, Fleischmann T, Kämpfer P, Kohler HPE (2007) Description of Sphingosinicella xenopeptidilytica sp. nov., a β-peptide degrading strain, and emended descriptions of the genus Sphingosinicella and the species Sphingosinicella microcystinivorans. Int J Syst Evol Microbiol 57:107–113

    CAS  PubMed  Google Scholar 

  • Gopi HN, Ravindra G, Pal PP, Pattanaik P, Balaram H, Balaram P (2003) Proteolytic stability of b-peptide bonds probed using quenched fluorescent substrates incorporating a hemoglobin cleavage site. FEBS Lett 535:175–178

    CAS  PubMed  Google Scholar 

  • Greenblatt HM, Almog O, Maras B, Spungin-Bialik A, Barra D, Blumberg S, Shoham G (1997) Streptomyces griseus aminopeptidase: X-ray crystallographic structure at 1.75 Å resolution. J Mol Biol 265:620–636

    CAS  PubMed  Google Scholar 

  • Hanson HT, Smith EL (1949) Carnosinase: an enzyme of swine kidney. J Biol Chem 179:789–801

    CAS  PubMed  Google Scholar 

  • Heck T, Limbach M, Geueke B, Zacharias M, Gardiner J, Kohler HPE, Seebach D (2006) Enzymatic degradation of β- and mixed α,β-oligopeptides. Chem Biodiv 3:1325–1348

    CAS  Google Scholar 

  • Hintermann T, Seebach D (1997) The biological stability of β-petides: no interactions between α-and β-peptidic structures? Chimia 50:244–247

    Google Scholar 

  • Hook DF, Gessier F, Noti C, Kast P, Seebach D (2004) Probing the proteolytic stability of β-peptides containing α-fluoro- and α-hydroxy-β-amino acids. Chembiochem 5:691–706

    CAS  PubMed  Google Scholar 

  • Jozic D, Bourenkow G, Bartunik H, Scholze H, Dive V, Henrich B, Huber R, Bode W, Maskos K (2002) Crystal structure of the dinuclear zinc aminopeptidase PepV from Lactobacillus delbrueckii unravels its preference for dipeptides. Structure 10:1097–1106

    CAS  PubMed  Google Scholar 

  • Juaristi E, Lopez-Ruiz H (1999) Recent advances in the enantioselective synthesis of β-amino acids. Curr Med Chem 6:983–1004

    CAS  PubMed  Google Scholar 

  • Kimmerlin T, Seebach D (2005) ‘100 years of peptide synthesis’: ligation methods for peptide and protein synthesis with applications to β-peptide assemblies. J Pept Res 65:229–260

    CAS  PubMed  Google Scholar 

  • Komeda H, Asano Y (2005) A DmpA-homologous protein from Pseudomonas sp. is a dipeptidase specific for b-alanyl dipeptides. FEBS J 272:3075–3084

    CAS  PubMed  Google Scholar 

  • Komeda H, Harada H, Washika S, Sakamoto T, Ueda M, Asano Y (2004) A novel R-stereoselective amidase from Pseudomonas sp. MCI3434 acting on piperazine-2-tert-butylcarboxamide. Eur J Biochem 271:1580–1590

    CAS  PubMed  Google Scholar 

  • Koyack MJ, Cheng RP (2006) Design and synthesis of β-peptides with biological activity. Methods Mol Biol 340:95–109

    CAS  PubMed  Google Scholar 

  • Lelais G, Seebach D (2003) Synthesis, CD spectra, and enzymatic stability of β2-oligoazapeptides prepared from (S)-2-hydrazino carboxylic acids carrying the side chains of Val, Ala, and Leu. Helv Chim Acta 86:4152–4168

    CAS  Google Scholar 

  • Lelais G, Seebach D (2004) β2-Amino acids-syntheses, occurrence in natural products, and components of β-peptides. Biopolymers 76:206–243

    CAS  PubMed  Google Scholar 

  • Liljeblad A, Kanerva LT (2006) Biocatalysis as a profound tool in the preparation of highly enantiopure β-amino acids. Tetrahedron 62:5831–5854

    CAS  Google Scholar 

  • Lind R, Greenhow D, Perry S, Kimmerlin T, Seebach D (2004) Comparative metabolism of α-and β-peptides in the insect Heliothis virescens and in plant cells of black Mexican sweet maize. Chem Biodiv 1:1391–1400

    CAS  Google Scholar 

  • Liu M, Sibi MP (2002) Recent advances in the stereoselective synthesis of β-amino acids. Tetrahedron 58:7991–8035

    CAS  Google Scholar 

  • Medrano FJ, Alonso J, Garcia JL, Romero A, Bode W, Gomis-Ruth FX (1998) Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family. EMBO J 17:1–9

    CAS  PubMed  PubMed Central  Google Scholar 

  • Miyazawa T, Minowa H, Imagawa K, Yamada T (2004) Separation of enantiomers of non-protein amino acids by high-performance liquid chromatography on a chiral ligand-exchange column. Chromatographia 60:45–50

    CAS  Google Scholar 

  • Obst M, Steinbüchel A (2004) Microbial degradation of poly(amino acid)s. Biomacromolecules 5:1166–1176

    CAS  PubMed  Google Scholar 

  • Oi N, Kitahara H, Kira R (1992) Direct separation of enantiomers by high-liquid performance liquid chromatography on a new chiral ligand-exchange phase. J Chromatogr 592:291–296

    CAS  Google Scholar 

  • Oinonen C, Rouvinen J (2000) Structural comparison of Ntn-hydrolases. Protein Sci 9:2329–2337

    CAS  PubMed  PubMed Central  Google Scholar 

  • Quinn PJ, Boldyrev AA, Formazuyk VE (1992) Carnosine: its properties, functions and potential therapeutic applications. Mol Aspects Med 13:379–444

    CAS  PubMed  Google Scholar 

  • Rawlings ND, Tolle DP, Barrett AJ (2004) MEROPS: the peptidase database. Nucleic Acids Res 32:D160–D164

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roderick SL, Matthews BW (1993) Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme. Biochemistry 32:3907–3912

    CAS  PubMed  Google Scholar 

  • Schreiber JV, Frackenpohl J, Moser F, Fleischmann T, Kohler HPE, Seebach D (2002) On the biodegradation of β-peptides. Chembiochem 3:424–432

    CAS  PubMed  Google Scholar 

  • Seebach D, Overhand M, Kühnle FNM, Martinoni B, Oberer L, Hommel U, Widmer H (1996) β-Peptides: synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a β-hexapeptide in solution and its stability towards pepsin. Helv Chim Acta 76:913–941

    Google Scholar 

  • Seebach D, Abele S, Schreiber JV, Martinoni B, Nussbaum AK, Schild H, Schulz H, Hennecke H, Woessner R, Bitsch F (1998) Biological and pharmacokinetic studies with β-peptides. Chimia 52:734–739

    CAS  Google Scholar 

  • Seebach D, Beck AK, Bierbaum DJ (2004) The world of β- and γ-peptides comprised of homologated proteinogenic amino acids and other components. Chem Biodiv 1:1111–1239

    CAS  Google Scholar 

  • Teufel M, Saudek V, Ledig JP, Bernhardt A, Boularand S, Carreau A, Cairns NJ, Carter C, Cowley DJ, Duverger D, Ganzhorn AJ, Guenet C, Heintzelmann B, Laucher V, Sauvage C, Smirnova T (2003) Sequence identification and characterization of human carnosinase and a closely related non-specific dipeptidase. J Biol Chem 278:6521–6531

    CAS  PubMed  Google Scholar 

  • Tillett D, Dittmann E, Erhard M, von Dohren H, Borner T, Neilan BA (2000) Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC7806: an integrated peptide-polyketide synthetase system. Chem Biol 7:753–764

    CAS  PubMed  Google Scholar 

  • Vongerichten KF, Klein JR, Matern H, Plapp R (1994) Cloning and nucleotide sequence analysis of pepV, a carnosinase gene from Lactobacillus delbrueckii subsp. lactis DSM 7290, and partial characterization of the enzyme. Microbiology 140:2591–2600

    CAS  PubMed  Google Scholar 

  • Wiegand H, Wirz B, Schweitzer A, Camenisch GP, Rodriguez Perez MI, Gross G, Woessner R, Voges R, Arvidsson PI, Frackenpohl J, Seebach D (2002) The outstanding metabolic stability of a 14C-labeled β-nonapeptide in rats-in vitro and in vivo pharmacokinetic studies. Biopharm Drug Dispos 23:251–262

    CAS  PubMed  Google Scholar 

  • Wiegand H, Wirz B, Schweitzer A, Gross G, Rodriguez Perez MI, Andres H, Kimmerlin T, Rueping M, Seebach D (2004) Pharmacokinetic investigation of a 14C-labelled β3/α-tetrapeptide in rats. Chem Biodiv 1:1812–1828

    CAS  Google Scholar 

  • Wood MR, Johnson P (1981) Purification of carnosine synthetase from avian muscle by affinity chromatography and determination of its subunit structure. Biochim Biophys Acta 662:138–144

    CAS  PubMed  Google Scholar 

Download references

Acknowledgment

This work was financially supported by the Swiss National Science Foundation grant SNF315200-109414/1 (B.G.).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to B. Geueke.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Geueke, B., Kohler, HP.E. Bacterial β-peptidyl aminopeptidases: on the hydrolytic degradation of β-peptides. Appl Microbiol Biotechnol 74, 1197–1204 (2007). https://doi.org/10.1007/s00253-007-0872-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-007-0872-5

Keywords

Navigation