Crystal structure of human renal dipeptidase involved in β-lactam hydrolysis

Journal of Molecular Biology

Volumn 321, Issue 2, 2002, Pages 177-184

  Nitanai, Yasushi ^a,c   Satow, Yoshinori ^a   Adachi, Hideki ^b   Tsujimoto, Masafumi ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^c RIKEN HARIMA INSTITUTE   (Japan)

Author keywords

Binuclear metal ions; Cilastatin complex; Crystal structure; Human renal dipeptidase; Metabolism of lactam antibiotics

Indexed keywords

125 GLUTAMIC ACID; ADENOSINE DEAMINASE; BACTERIAL ENZYME; BETA LACTAM ANTIBIOTIC; CARBOHYDRATE; CILASTATIN; DIPEPTIDASE; DIPEPTIDE; LIGAND; METAL ION; UNCLASSIFIED DRUG; UREASE; ZINC ION;

ALPHA CHAIN; AMINO ACID SEQUENCE; ARTICLE; BETA CHAIN; BINDING SITE; CATALYSIS; CELL NUCLEUS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIMERIZATION; DRUG DESIGN; DRUG INHIBITION; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME STRUCTURE; HYDROLYSIS; KIDNEY; KIDNEY TUBULE; MICROVILLUS; MOLECULE; NONHUMAN; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS); MURINAE;

EID: 0036382767     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00632-0     Document Type: Article

References (33)

1. Adachi, H., Tawaragi, Y., Inuzuka, C., Kubota, I., Tsujimoto, M., Nishihara, T. & Nakazato, H. (1990). Primary structure of human microsomal dipeptidase deduced from molecular cloning. J. Biol. Chem. 265, 3992-3995.
2. Campbell, B. J., Lin, Y. C., Davis, R. V. & Ballew, E. (1966). The purification and properties of a particulate renal dipeptidase. Biochim. Biophys. Acta, 118, 371-386.
3. Littlewood, G. M., Hooper, N. M. & Turner, A. J. (1989). Ectoenzymes of the kidney microvillar membrane. Biochem. J. 257, 361-367.
4. Jongeneel, C. V., Bouvier, J. & Bairoch, A. (1989). A unique signature identifies a family of zinc-dependent metallopeptidases. FEBS Letters, 242, 211-214.
5. Adachi, H., Katayama, T., Nakazato, H. & Tsujimono, M. (1993). Importance of Glu-125 in the catalytic activity of human renal dipeptidase. Biochim. Biophys. Acta, 1163, 42-48.
6. 219is critical but DHXXH motif is no essential for zinc binding or catalytic activity. FEBS Letters, 349, 50-54.
7. Keynan, S., Hooper, N. M. & Turner, A. J. (1997). Identification by site-directed mutagenesis of three essential histidine residues in membrane dipeptidase, a novel mammalian zinc peptidase. Biochem. J. 326, 47-51.
8. Kahan, F. M., Kropp, H., Sundelof, J. G. & Birnbaum, J. (1983). Thienamycin: development of imipenencilastatin. J. Antimicrob. Chemother. 12, 1-35.
9. Kropp, H., Sundelof, J. G., Hajdu, R. & Kahan, F. M. (1982). Metabolism of thienamycin and related carbapenem antibiotics by the renal dipeptidase, dehydropeptidase. Antimicrob. Agents Chemother. 22, 62-70.
10. Kim, H. S. & Campbell, B. J. (1982). beta-Lactamase activity of renal dipeptidase against N-formimidoylthienamycin. Biochem. Biophys. Res. Commun. 108, 1638-1642.
11. Adachi, H., Kubota, I., Okamura, N., Iwata, H., Tsujimoto, M., Nakazato, H. et al. (1989). Purification and characterization of human microsomal dipeptidase. J. Biochem. (Tokyo), 105, 957-961.
12. Igarashi, P. & Karniski, L. P. (1991). Cloning of cDNAs encoding a rabbit renal brush border membrane protein immunologically related to band 3. Sequence similarity with microsomal dipeptidase. Biochem. J. 280, 71-78.
13. Rached, E., Hooper, N. M., James, P., Semenza, G., Turner, A. J. & Mantei, N. (1990). cDNA cloning and expression in Xenopus laevis oocytes of pig renal dipeptidase, a glycosyl-phosphatidylinositol-anchored ectoenzyme. Biochem. J. 271, 755-760.
14. 4. Biochim. Biophys. Acta, 1226, 337-340.
15. Adachi, H., Ishida, N. & Tsujimoto, M. (1992). Primary structure of rat renal dipeptidase and expression of its mRNA in rat tissues and COS-1 cells. Biochim. Biophys. Acta, 1132, 311-314.
16. Satoh, S., Keida, Y., Konta, Y., Maeda, M., Matsumoto, Y., Niwa, M. & Kohsaka, M. (1993). Purification and molecular cloning of mouse renal dipeptidase. Biochim. Biophys. Acta, 1163, 234-242.
17. Adachi, H. & Tsujimoto, M. (1995). Cloning and expression of dipeptidase from Acinetobacter calcoaceticus ATCC 23055. Biochemistry, 118, 555-561.
18. Nitanai, Y., Satow, Y., Adachi, H. & Tsujimono, M. (1996). Crystallization and preliminary X-ray investigation of a glycoprotein, human renal dipeptidase. J. Cryst. Growth, 168, 280-283.
19. Keynan, S., Habgood, N. T., Hooper, N. M. & Turner, A. J. (1996). Site-directed mutagenesis of conserved cysteine residues in porcine membrane dipeptidase. Cys361 alone is involved in disulfide-linked dimerization. Biochemistry, 35, 12511-12517.
20. Armstrong, D. D., Mukhopadhyay, S. K. & Campbell, B. J. (1974). Physicochemical characterization of renal dipeptidase. Biochemistry, 13, 1745-1750.
21. Campbell, B. J., Shih, Y. D., Forrester, L. J. & Zahler, W. L. (1988). Specificity and inhibition studies of human renal dipeptidase. Biochim. Biophys. Acta, 956, 110-118.
22. Wang, Z. & Quiocho, F. A. (1998). Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity. Biochemistry, 37, 8314-8324.
23. Jabri, E., Carr, M. B., Hausinger, R. P. & Karplus, P. A. (1995). The crystal structure of urease from Klebsiella aerogenes. Science, 258, 998-1004.
24. Benning, M. M., Hong, S. B., Raushel, F. M. & Holden, E. M. (2000). The binding of substrate analogs to phosphotriesterase. J. Biol. Chem. 275, 30556-30560.
25. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
26. Otwinowski, Z. (1993). DENZO and SCALEPACK, Data Processing and Scaling Program, Yale University, New Haven, CT, USA.
27. Collaborative Computational Project Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallog. D50, 760-763.
28. Roussel, A. & Cambillau, C. (1995). TURBO-FRODO Version 5.4, Faculté de Médecine Nord, Marseille, France.
29. Brünger, A. T. (1992). X-PLOR Version 3.1: A System for X-ray Crystallography and NMR, Yale University, New Haven, CT, USA.
30. Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
31. Merritt, E. A. & Murphy, M. E. P. (1994). Raster3D Version 2.0: a program for photorealistic molecular graphics. Acta Crystallog. D50, 869-873.
32. McRee, D. E. (1993). Practical Protein Crystallography, Academic Press, San Diego, CA, USA.
33. Nicholls, A., Sharp, K. A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11, 281-296.