Structural and biochemical characterization of a novel aminopeptidase from human intestine

Journal of Biological Chemistry

Volumn 290, Issue 18, 2015, Pages 11321-11336

  Tykvart, Jan ^a,b   Bařinka, Cyril ^c   Svoboda, Michal ^a,b   Navrátil, Václav ^a,b   Souček, Radko ^a   Hubálek, Martin ^a   Hradilek, Martin ^a   Šácha, Pavel ^a,b   Lubkowski, Jacek ^d   Konvalinka, Jan ^a,b  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

^c INSTITUTE OF BIOTECHNOLOGY   (Czech Republic)

^d NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES;

AMINO PEPTIDASE; BIOCHEMICAL CHARACTERIZATION; CARBOXYPEPTIDASE; HUMAN INTESTINE; METALLOPEPTIDASES; SMALL INTESTINE; SUBSTRATE SPECIFICITY; X-RAY STRUCTURE;

PROTEINS;

AMINOPEPTIDASE; DIPEPTIDYL PEPTIDASE IV; GLUTAMATE CARBOXYPEPTIDASE II; HUMAN ILEAL AMINOPEPTIDASE; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; UNCLASSIFIED DRUG; PROTEINASE;

ALTERNATIVE RNA SPLICING; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME SPECIFICITY; GENE EXPRESSION; HUMAN; HUMAN TISSUE; NAALADL1 GENE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; SEQUENCE ALIGNMENT; SMALL INTESTINE ABSORPTION; AMINO ACID SEQUENCE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; INTESTINE; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; RAT; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CRYSTALLOGRAPHY, X-RAY; DIPEPTIDYL PEPTIDASE 4; ENDOPEPTIDASES; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GLUTAMATE CARBOXYPEPTIDASE II; HUMANS; INTESTINES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RATS;

EID: 84929460052     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M114.628149     Document Type: Article

References (31)

1. Pangalos, M. N., Neefs, J. M., Somers, M., Verhasselt, P., Bekkers, M., van der Helm, L., Fraiponts, E., Ashton, D., and Gordon, R. D. (1999) Isolation and expression of novel human glutamate carboxypeptidases with N-acetylated a-linked acidic dipeptidase and dipeptidyl peptidase IV activity. J. Biol. Chem. 274, 8470-8483
2. Shneider, B. L., Thevananther, S., Moyer, M. S., Walters, H. C, Rinaldo, P., Devarajan, P., Sun, A. Q., Dawson, P. A., and Ananthanarayanan, M. (1997) Cloning and characterization of a novel peptidase from rat and human ileum. J. Biol. Chem. 272, 31006-31015
3. Barinka, C, Rinnova, M., Sacha, P., Rojas, C, Majer, P., Slusher, B. S., and Konvalinka, J. (2002) Substrate specificity, inhibition and enzymological analysis of recombinant human glutamate carboxypeptidase II. J. Neuro-chem. 80, 477-487
4. Hlouchova, K., Barinka, C, Klusak, V., Sacha, P., Mlcochova, P., Majer, P., Ruĺisek, L., and Konvalinka, J. (2007) Biochemical characterization of human glutamate carboxypeptidase III.J. Neurochem. 101, 682-696
5. Tykvart, J., Sacha, P., Barinka, C, Knedĺik, T., Starkova, J., Lubkowski, J., and Konvalinka, J. (2012) Efficient and versatile one-step affinity purification of in vivo biotinylated proteins: expression, characterization and structure analysis of recombinant human glutamate carboxypeptidase II. Protein Expr. Purif. 82, 106-115
6. Koźisek, M., Saskova, K. G., Rezacova, P., Brynda, J., van Maarseveen, N. M., De Jong, D., Boucher, C. A., Kagan, R. M., Nijhuis, M., and Konvalinka, J. (2008) Ninety-nine is not enough: molecular characterization of inhibitor-resistant human immunodeficiency virus type 1 protease mutants with insertions in the flap region. J. Virol. 82, 5869-5878
7. Langone, J. J., and Van Vunakis, H. (1986) Immunological techniques. Part I. Hybridoma technology and monoclonal antibodies. Methods Enzymol. 121, 1-947
8. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
9. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Sto-roni, L. C, and Read, R. J. (2007) Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674
10. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
11. Emsley, P., and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
12. Chen, V. B., Arendall, W. B., 3rd, Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., and Richardson, D. C. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12-21
13. Rovenska, M., Hlouchova, K., Sacha, P., Mlcochova, P., Horak, V., Zamecńik, J., Barinka, C, and Konvalinka, J. (2008) Tissue expression and enzymologic characterization of human prostate specific membrane antigen and its rat and pig orthologs. Prostate 68, 171-182
14. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254
15. Barlos, K., Chatzi, O., Gatos, D., and Stavropoulos, G. (1991) 2-Chlorotri-tyl chloride resin: studies on anchoring of Fmoc-amino acids and peptide cleavage. Int. J. Pept. Protein Res. 37, 513-520
16. Kaiser, E., Colescott, R. L., Bossinger, C. D., and Cook, P. I. (1970) Color test for detection of free terminal amino groups in the solid-phase synthesis of peptides. Anal. Biochem. 34, 595-598
17. Woodward, C, Henderson, J. K., and Wielgos, T. (2007) High-speed Amino Acid Analysis (AAA) on 1.8/nm Reversed-phase (RP) Columns. Agilent Technologies Application Note 5989-6297EN, Agilent Technologies, Inc., Wilmington, DE
18. Schilling, O., Huesgen, P. F., Barre, O., Auf dem Keller, U., and Overall, C. M. (2011) Characterization of the prime and non-prime active site specificities of proteases by proteome-derived peptide libraries and tandem mass spectrometry. Nat Protoc. 6, 111-120
19. Krissinel, E. (2012) Enhanced fold recognition using efficient short fragment clustering. J. Mol. Biochem. 1, 76-85
20. Mesters, J. R., Barinka, C, Li, W., Tsukamoto, T., Majer, P., Slusher, B. S., Konvalinka, J., and Hilgenfeld, R. (2006) Structure of glutamate carboxy-peptidase II, a drug target in neuronal damage and prostate cancer. EMBO J. 25, 1375-1384
21. Pavĺicek, J., Ptacek, J., and Barinka, C (2012) Glutamate carboxypeptidase II: an overview of structural studies and their importance for structure-based drug design and deciphering the reaction mechanism of the enzyme. Curr. Med. Chem. 19, 1300-1309
22. Lawrence, C M., Ray, S., Babyonyshev, M., Galluser, R., Borhani, D. W., and Harrison, S. C (1999) Crystal structure of the ectodomain of human transferrin receptor. Science 286, 779-782
23. Zheng, H, Chruszcz, M., Lasota, P., Lebioda, L., and Minor, W. (2008) Data mining of metal ion environments present in protein structures. J. Inorg. Biochem. 102, 1765-1776
24. Klusak, V., Barinka, C, Plechanovova, A., Mlcochova, P., Konvalinka, J., Ruĺisek, L., and Lubkowski, J. (2009) Reaction mechanism of glutamate carboxypeptidase II revealed by mutagenesis, X-ray crystallography, and computational methods. Biochemistry 48, 4126-4138
25. Navratil, M., Ptacek, J., Sácha, P., Starkova, J., Lubkowski, J., Barinka, C, and Konvalinka, J. (2014) Structural and biochemical characterization of the folyl-poly-7-L-glutamate hydrolyzing activity of human glutamate carboxypeptidase II. FEBS J. 281, 3228-3242
26. Lindner, H. A., Lunin, V. V., Alary, A., Hecker, R., Cygler, M., and Menard, R. (2003) Essential roles of zinc ligation and enzyme dimerization for catalysis in the aminoacylase-1/M20 family. J. Biol. Chem. 278, 44496-44504
27. Thierry-Mieg, D., and Thierry-Mieg, J. (2006) AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 7, S12.1-14
28. Sedo, A., and Maĺik, R. (2001) Dipeptidyl peptidase IV-like molecules: homologous proteins or homologous activities? Biochim. Biophys. Acta 1550, 107-116
29. Taylor, A. (1996) in The Aminopeptidases (Taylor, A, ed) pp. 1-20, Lan-des Bioscience Publishers, Austin, TX
30. Weiss, M. S. (2001) Global indicators of X-ray data quality. J. Appl. Crys-tallogr. 34, 130-135
31. Cheng, Y., and Prusoff, W. H. (1973) Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem. Pharmacol. 22, 3099-3108