Structural evidence that puromycin hydrolase is a new type of aminopeptidase with a prolyl oligopeptidase family fold

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 10, 2011, Pages 2999-3005

  Matoba, Yasuyuki ^a   Nakayama, Akira ^a   Oda, Kosuke ^a   Noda, Masafumi ^a   Kumagai, Takanori ^a   Nishimura, Motohiro ^b   Sugiyama, Masanori ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

^b YASUDA WOMEN'S UNIVERSITY   (Japan)

Author keywords

Aminopeptidase; Blasticidin S; Crystal structure; POP family; Puromycin

Indexed keywords

AMINOPEPTIDASE; PROLYL ENDOPEPTIDASE; PUROMYCIN HYDROLASE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; PRIORITY JOURNAL; PROTEIN FOLDING;

AMINOPEPTIDASES; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; HYDROLASES; NUCLEOSIDES; PUROMYCIN; SERINE ENDOPEPTIDASES; STREPTOMYCES;

EID: 80052604136     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23139     Document Type: Article

References (30)

1. Jardetzky O. Proton magnetic resonance of purine and pyrimidine derivatives. X. The conformation of puromycin. J Am Chem Soc 1963; 85: 1823-1825.
2. Yamaguchi H, Yamamoto C, Tanaka N. Inhibition of protein synthesis by blasticidin S. I. Studies with cell-free systems from bacterial and mammalian cells. J Biochem 1965; 57: 667-677.
3. Sugiyama M, Takeda A, Paik SY, Nimi O, Nomi R. Acetylation of blasticidin S by its producing actinomycetes. J Antibiot 1986; 39: 827-832.
4. Nishimura M, Matsuo H, Sugiyama M. Blasticidin S-producing Streptomyces morookaensis possesses an enzyme activity which hydrolyzes puromycin. FEMS Microbiol Lett 1995; 132: 95-100.
5. Nishimura M, Matsuo H, Nakamura A, Sugiyama M. Purification and characterization of a puromycin-hydrolyzing enzyme from blasticidin S-producing Streptomyces morookaensis. J Biochem 1998; 123: 247-252.
6. Sarid S, Berger A, Katchalski E. Proline iminopeptidase. J Biol Chem 1959; 234: 1740-1744.
7. Nishimura M, Ikeda K, Sugiyama M. Molecular cloning and characterization of gene encoding novel puromycin-inactivating enzyme from blasticidin S-producing Streptomyces morookaensis. J Biosci Bioeng 2006; 101: 63-69.
8. Polgár L. The prolyl oligopeptidase family. Cell Mol Life Sci 2002; 59: 349-362.
9. Wilk S. Prolyl endopeptidase. Life Sci 1980; 33: 2149-2157.
10. Polgár L. A potential processing enzyme in prokaryotes: oligopeptidase B, a new type of serine peptidase. Proteins 1997; 28: 375-379.
11. Kenny AJ, Booth AG, George SG, Ingram J, Kershaw D, Wood EJ, Young AR. Dipeptidyl peptidase IV, a kidney brush-border serine peptidase. Biochem J 1976; 157: 169-182.
12. Banbula A, Mak P, Bugno M, Silberring J, Dubin A, Nelson D, Travis J, Potempa J. Prolyl tripeptidyl peptidase from Porphyromonas gingivalis. A novel enzyme with possible pathological implications for the development of periodontitis. J Biol Chem 1999; 274: 9246-9252.
13. Kobayashi K, Smith JA. Acyl-peptide hydrolase from rat liver. Characterization of enzyme reaction. J Biol Chem 1987; 262: 11435-11445.
14. Usuki H, Uesugi Y, Iwabuchi M, Hatanaka T. Putative "acylaminoacyl" peptidases from Streptomyces griseus and S. coelicolor display "aminopeptidase" activities with distinct substrate specificities and sensitivities to reducing reagent. Biochim Biophys Acta 2009; 1794: 468-475.
15. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997; 276: 307-326.
16. de la Fottelle E, Bricogne G. Maximum-likelihood heavy-atom parameters refinement in the MIR and MAD methods. Methods Enzymol 1997; 276: 472-494.
17. McRee DE. A visual protein crystallographic software system for X11/XView. J Mol Graphics 1992; 10: 44-46.
18. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr Sect D Biol Crystallogr 1998; 54: 905-921.
19. Brünger AT. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992; 355: 472-475.
20. Fülöp V, Böcskei Z, Polgár L. Prolyl oligopeptidase: an unusual β-propeller domain regulates proteolysis. Cell 1998; 94: 161-170.
21. Rasmussen HB, Branner S, Wiberg FC, Wagtmann N. Crystal structure of human dipeptidyl peptidase IV/CD26 in complex with a substrate analog. Nat Struct Biol 2003; 10: 19-25.
22. Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto, T. Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis. J Mol Biol 2006; 362: 228-240.
23. Bartlam M, Wang G, Yang H, Gao R, Zhao X, Xie G, Cao S, Feng Y, Rao Z. Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1. Structure 2004; 12: 1481-1488.
24. Medrano FJ, Alonso J, García JL, Romero A, Bode W, Gomis-Rüth FX. Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family. EMBO J 1998; 17: 1-9.
25. Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002; 417: 141-147.
26. Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura, S. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nature Biotechnol 2003; 21: 526-531.
27. Kim H, Lipscomb WN. X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state. Biochemistry 1993; 32: 8465-8478.
28. Lowther WT, Orville AM, Madden DT, Lim S, Rich DH, Matthews BW. Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis. Biochemistry 1999; 38: 7678-7688.
29. Stamper CC, Bienvenue DL, Bennett B, Ringe D, Petsko GA, Holz RC. Spectroscopic and X-ray crystallographic characterization of bestatin bound to the aminopeptidase from Aeromonas (Vibrio) proteolytica. Biochemistry 2004; 43: 9620-9628.
30. Ito K, Nakajima Y, Onohara Y, Takeo M, Nakashima K, Matsubara F, Ito T, Yoshimoto T. Aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli: crystal structure and conformational change of the methionine 260 residue involved in substrate recognition. J Biol Chem 2006; 281: 33664-33676.