Determination of the MurD mechanism through crystallographic analysis of enzyme complexes

Journal of Molecular Biology

Volumn 289, Issue 3, 1999, Pages 579-590

  Bertrand, Jay A ^a   Auger, Geneviève ^b   Martin, Lydie ^a   Fanchon, Eric ^a   Blanot, Didier ^b   Le Beller, Dominique ^c   Van Heijenoort, Jean ^b   Dideberg, Otto ^a  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^b CNRS   (France)

^c Service de Biochimie   (France)

Author keywords

ADP ligase; Crystal structure; Drug design; Enzymatic mechanism; Peptidoglycan

Indexed keywords

ADENOSINE DIPHOSPHATE; GLUTAMIC ACID; LIGASE; MAGNESIUM ION; PHOSPHATE;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ANALYSIS; NONHUMAN; PRIORITY JOURNAL;

ESCHERICHIA COLI; NEGIBACTERIA; UMA;

EID: 0033546272     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2800     Document Type: Article

References (31)

1. Auger, G., Martin, L., Bertrand, J., Ferrari, P., Fanchon, E., Vaganay, S., Pétillot, Y., van Heijenoort, J., Blanot, D. & Dideberg, O. (1998). Large-scale preparation, purification, and crystallization of UDP-N-acetylmuramoyl-L-glutamate ligase from Escherichia coli. Protein Expr. Purif. 13, 23-29.
2. Bertrand, J. A., Auger, G., Fanchon, E., Martin, L., Blanot, D., van Heijenoort, J. & Dideberg, O. (1997). Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. EMBO J. 16, 3416-3425.
3. Bouhss, A., Mengin-Lecreulx, D., Blanot, D., van Heijenoort, J. & Parquet, C. (1997). Invariant amino acids in the Mur peptide synthetases of bacterial peptidoglycan synthesis and their modification by site-directed mutagenesis in the UDP-MurNAc: L-alanine ligase from Escherichia coli. Biochemistry, 36, 11556-11563.
4. Brünger, A. T. (1992a). Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-475.
5. Brünger, A. T. (1992b). X-PLOR Version 3. 1: A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.
6. CCP4, (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallog. Sect. D, 50, 760-763.
7. Fan, C., Park, I-S., Walsh, C. T. & Knox, J. R. (1997). D-alanine:D-alanine ligase: Phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Biochemistry, 36, 2531-2538.
8. Gegnas, L. D., Waddell, S. T., Chabin, R. M., Reddy, S. & Wong, K. K. (1998). Inhibitors of the bacterial cell wall biosynthesis enzyme MurD. Bioorg. Med. Chem. Letters, 8, 1643-1648.
9. Hara, T., Kato, H., Katsube, Y. & Oda, J. (1996). A pseudo-Michaelis quaternary complex in the reverse reaction of a ligase: Structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 Å resolution. Biochemistry, 35, 11967-11974.
10. Huang, W., Jia, J., Gibson, K. J., Taylor, W. S., Rendina, A. R., Schneider, G. & Lindqvist, Y. (1995). Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate. Biochemistry, 34, 10985-10995.
11. Jabri, E., Carr, M. B., Hausinger, R. P. & Karplus, P. A. (1995). The crystal structure of urease from Klebsiella aerogenes. Science, 268, 998-1004.
12. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. Sect. D, 47, 110-119.
13. Kabsch, W. (1988). Evaluation of single crystal X-ray diffraction data from a position sensitive detector. J. Appl. Crystallog. 21, 916-924.
14. Kjeldgaard, M., Nissen, P., Thirup, S. & Nyborg, J. (1993). The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure, 1, 35-50.
15. Kraulis, P. J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
16. Lundqvist, T. & Schneider, G. (1991). Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its substrate, ribulose-1,5-bisphosphate. J. Biol. Chem. 266, 12604-12611.
17. Moy, J.-P. (1994). A 200 mm input field, 5-80 keV detector based on an X-ray image intensifier and CCD camera. Nucl. Instrum. Meth. Phys. Res. Sect. A, 348, 641-644.
18. Nathenson, S. G., Strominger, J. L. & Ito, E. (1964). Enzymatic synthesis of the peptide in bacterial uridine nucleotides. IV. Purification and properties of the D-glutamic acid-adding enzyme. J. Biol. Chem. 239, 1773-1776.
19. Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology (Carter, C. W., Jr & Sweet, R. M., eds), vol. 276, pp. 307-326, Academic Press, New York, USA.
20. Pai, E. F., Krengel, U., Petsko, G. A., Goody, R. S., Kabsch, W. & Wittinghofer, A. (1990). Refined crystal structure of the triphosphate conformation of H-ras-p21 at 1.35 Å resolution: Implications for the mechanism of GTP hydrolysis. EMBO J. 9, 2351-2359.
21. Poland, B. W., Hou, Z., Bruns, C., Fromm, H. J. & Honzatko, R. B. (1996). Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli. J. Biol. Chem. 271, 15407-15413.
22. Pratviel-Sosa, F., Mengin-Lecreulx, D. & van Heijenoort, J. (1991). Over-production, purification and properties of the uridine diphosphate N-acetylmuramoyl- L-alanine:D-glutamate ligase from Escherichia coli. Eur. J. Biochem. 202, 1169-1176.
23. Pratviel-Sosa, F., Acher, F., Trigalo, F., Blanot, D., Azerad, R. & van Heijenoort, J. (1994). Effect of various analogues of D-glutamic acid on the D-glutamate-adding enzyme from Escherichia coli. FEMS Microbiol. Letters, 115, 223-228.
24. Ramachandran, G. N., Ramakrishnan, C. & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95-99.
25. Ray, W. J., Jr, Bolin, J. T., Puvathingal, J. M., Minor, W., Liu, Y. W. & Muchmore, S. W. (1991). Removal of salt from a salt-induced protein crystal without cross-linking. Preliminary examination of "desalted" crystals of phosphoglucomutase by X-ray crystallography at low temperature. Biochemistry, 30, 6866-6875.
26. Shi, Y. & Walsh, C. T. (1995). Active site mapping of Escherichia coli D-Ala-D-Ala ligase by structure-based mutagenesis. Biochemistry, 34, 2768-2776.
27. Suzuki, Y., Shimizu, T., Morii, H. & Tanokura, M. (1997). Hydrolysis of AMPPNP by the motor domain of ncd, a kinesin-related protein. FEBS Letters, 409, 29-32.
28. Tanner, M. E., Vaganay, S., van Heijenoort, J. & Blanot, D. (1996). Phosphinate inhibitors of the D-glutamic acid-adding enzyme of peptidoglycan biosynthesis. J. Org. Chem. 61, 1756-1760.
29. 2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions. Nature Struct. Biol. 4, 990-994.
30. Vaganay, S., Tanner, M. E., van Heijenoort, J. & Blanot, D. (1996). Study of the reaction mechanism of the D-glutamic acid-adding enzyme from Escherichia coli. Microb. Drug Resist. 2, 51-54.
31. Wittinghofer, A. (1997). Signaling mechanistics: Aluminum fluoride for molecule of the year. Curr. Biol. 7, R682-R685.