Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase

Journal of Molecular Biology

Volumn 266, Issue 2, 1997, Pages 381-399

  Lawrence, M C ^a   Barbosa, J A R G ^a   Smith, B J ^a   Hall, N E ^a   Pilling, P A ^a   Ooi, H C ^b   Marcuccio, S M ^b  

^a CSIRO   (Australia)

^b Biomolecular Research Institute   (Australia)

Author keywords

( )8 barrel; Enzyme inhibitors; N acetylneuraminate lyase; Protein structure; Schiff base formation

Indexed keywords

LYASE; N ACETYLNEURAMINATE LYASE; SCHIFF BASE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STEREOCHEMISTRY;

EID: 0031581884     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0769     Document Type: Article

References (67)

1. Aisaka K., Igarashi A., Yamaguchi K., Uwajima T. Purification, crystallization and characterization of N -acetylneuraminate lyase from Escherichia coli. Biochem. J. 276:1991;541-546.
2. Barnsley E. A. Naphthalene metabolism by Pseudomonads: the oxidation of 1,2-dihydroxynaphthalene to 2-hydroxychromene-2-carboxylic acid and the formation of 2′-hydroxybenzalpyruvate. Biochem. Biophys. Res. Commun. 72:1976;1116-1121.
3. 1H-NMR investigations on stereochemistry, kinetics and mechanism. Biol. Chem. Hoppe-Seyler. 370:1989;141-149.
4. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
5. Blumenthal H. J., Fish D. C. Bacterial conversion of D -glucarate to glycerate and pyruvate. Biochem. Biophys. Res. Commun. 11:1963;239-243.
6. Bonnassie S., Oreglia J., Sicard A. M. Nucleotide sequence of the dapA gene from Corynebacterium glutamicum. Nucl. Acids Res. 18:1990;6421.
7. Brändén C.-I. The TIM barrel: the most frequently occurring folding motif in proteins. Curr. Opin. Struct. Biol. 1:1991;978-983.
8. Brunetti P., Swanson A., Roseman S. Enzymatic determination of sialic acids. Methods in Enzymology. 1963;Academic Press, New York.
9. Brünger A. X-PLOR (version 3.1) Manual. 1992;Yale University Press, New Haven, London.
10. Chen N.-Y., Jiang S.-Q., Klein D. A., Paulus H. Organization and nucleotide sequence of the Bacillus subtilis diaminopimelate operon, a cluster of genes encoding the first three enzymes of diaminopimelate synthesis and dipicolinate synthase. J. Biol. Chem. 268:1993;9448-9465.
11. Chothia C. One thousand families for the molecular biologist. Nature. 357:1993;543-544.
12. Dagley S., Trudgill P. W. The metabolism of galactarate, D -glucarate and various pentoses by species of Pseudomonas. Biochem. J. 95:1965;48-58.
13. Deijl C. M., Vliegenthart J. F. G. Configuration of substrate and products of N -acetylneuraminate pyruvate-lyase from Clostridium perfringens. Biochem. Biophys. Res. Commun. 111:1983;668-674.
14. Devereux J., Haerbli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucl. Acids Res. 12:1984;387-395.
15. DeVries G. H., Binkley S. B. N -Acetylneuraminic acid aldolase of Clostridium perfringens: purification, properties and mechanism of action. Arch. Biochem. Biophys. 151:1972a;234-242.
16. DeVries G. H., Binkley S. B. 3-Hydroxy- N -acetylneuraminic acid: synthesis and inhibitory properties. Arch. Biochem. Biophys. 151:1972b;243-250.
17. Eaton R. W. Organization and evolution of haphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o -hydroxychromene-2-carboxylate isomerase and trans-o -hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J. Bacteriol. 176:1994;7757-7762.
18. Eaton R. W., Chapman P. J. Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxy-naphthalene and subsequent reactions. J. Bacteriol. 174:1992;7542-7554.
19. Engh R. A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog. sect. A. 47:1991;392-400.
20. Farber G. K. An α/β-barrel full of evolutionary trouble. Structure. 3:1993;409-412.
21. Farber G. K., Petsko G. The evolution of α/β-barrel enzymes. Trends Biochem. Sci. 15:1990;228-234.
22. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
23. -auxotroph. Mol. Gen. Genet. 228:1991;287-293.
24. Geirsson J. K. F., Gudmundsdottir A. D. Reactions of 1-aza-1,3-butadienes. A convenient synthesis of N -benzyl-1,4-dihydropyridines. Acta Chem. Scand. 43:1989;618-619.
25. Giovannini A., Savoia D., Umani-Ronchi A. Organometallic ring-opening reactions of N -acyl and N -alkoxycarbonyl lactams. Synthesis of cyclic imines. J. Org. Chem. 54:1989;228-234.
26. Hennig M., Schlesier B., Dauter Z., Pfeffer S., Betzel C., Höhne W. E., Wilson K. S. A TIM barrel protein without enzymatic activity? Crystal structure of narbonin at 1.8 Å resolution. FEBS Letters. 306:1992;80-84.
27. Izard T., Lawrence M. C., Malby R., Lilley G. G., Colman P. M. The three-dimensional structure of N -acetylneuraminate lysase from Escherichia coli. Structure. 2:1994;361-369.
28. 8-barrel enzymes: chance or homology? Protein Sci. 4:1995;1239-1242.
29. 8-barrel enzymes as a possible indicator of their evolutionary relatedness. Protein Eng. 8:1995;809-813.
30. Jeffcoat R., Hassall H., Dagley S. The metabolism of D -glucarate by Pseudomonas acidovorans. Biochem. J. 115:1969a;969-976.
31. Jeffcoat R., Hassall H., Dagley S. Purification and properties of the D -4-deoxy-5-oxoglucarate hydro-lyase (decarboxylating). Biochem. J. 115:1969b;977-983.
32. Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86-89.
33. Jones T. A., Jou J.-Y., Cowan S. W. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
34. Kaneko T., Hashimoto T., Kumpaisal R., Yamada Y. Molecular cloning of wheat dihydrodipicolinate synthase. J. Biol. Chem. 265:1990;17451-17455.
35. Kaneko T., Tanaka A., Sato S., Kotani H., Sazuka T., Miyajima N., Sugiura M., Tabata S. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome. DNA Res. 2:1995;153-166.
36. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallog. 24:1991;946-950.
37. Kuhm A. E., Knackmuss H.-J., Stolz A. Purification and properties of 2′-hydroxybenzalpyruvate aldolase from a bacterium that degrades naphthalenesulfonates. J. Biol. Chem. 268:1993;9484-9489.
38. Laber B., Gomis-Rüth F.-X., Romao M. J., Huber R. Escherichia coli dihydrodipicolinate synthase, identification of the active site and crystallization. Biochem. J. 288:1992;691-695.
39. Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
40. Lebioda L., Hatada M. H., Tulinsky A., Mavridis I. M. Comparison of the folding of 2-keto-3-deoxy-6-phosphogluconate aldolase, triosephosphate isomerase and pyruvate kinase. J. Mol. Biol. 162:1982;445-458.
41. Lesk A. M., Brändén C.-I., Chothia C. Structural principles of (α/β) barrel proteins: the packing of the interior of the sheet. Proteins: Struct. Funct. Genet. 8:1989;139-148.
42. Lorenz M., Partensky F., Boerner T., Hess W. R. Sequencing of RAPD fragments amplified from the genome of the prokaryote Prochlorococcus marinus (Prochlorophyta). Biochem. Mol. Biol. Int. 36:1995;705-713.
43. Luzzati V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallog. 23:1952;50-54.
44. Mavridis I. M., Hatada M. H., Tulinsky A., Lebioda L. Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2.8 Å resolution. J. Mol. Biol. 162:1982;419-444.
45. Meysick K., Dimock K., Garber G. E. Molecular characterization and expression of a N -acetylneuraminate lyase gene from Trichomonas vaginalis. Mol. Biochem. Parasitol. 76:1996;289-292.
46. Mirwaldt C., Körndorfer I., Huber R. The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 Å resolution. J. Mol. Biol. 246:1995;227-239.
47. Mulzer J., Brüntrup G. Decarboxylative dehydration of β-hydroxycarboxylic acids by redox condensation: a novel olefin synthesis. Angew. Chem. Int. Ed. Engl. 16:1977;255-256.
48. Mulzer J., Lammer O. Olefins from β-hydroxycarboxylic acids: synthesis of isomerically pure α- and β-asarone. Angew. Chem. Int. Ed. Engl. 22:1983;628-629.
49. Murphy P. J., Trenz S. P., Grzemski W., De Bruijn F. J., Schell J. The Rhizobium meliloti rhizopine mos locus is a mosaic structure facilitating its symbiotic regulation. J. Bacteriol. 175:1993;5193-5204.
50. Ogasawara N., Fujita Y., Kobayashi Y., Sadaie Y., Tanaka T., Takahashi H., Yamane K., Yoshikawa H. Systematic sequencing of the Bacillus subtilis genome: progress report of the Japanese group. Microbiology. 141:1995;257-259.
51. Ohta Y., Watanabe K., Kimura A. Complete nucleotide sequence of the E. coli N -acetylneuraminate lyase. Nucl. Acids Res. 13:1985;8843-8852.
52. Orenga C. Classification of protein folds. Curr. Opin. Struct. Biol. 4:1994;429-440.
53. Otwinowski Z. Oscillation data reduction program. Sawyer L., Isaacs N., Bailey S. Proceedings of the CCP4 Study Weekend: Data Collection and Processing. 1993;SERC Daresbury Laboratory.
54. Pearson W. R., Lipman D. J. Improved tools for biological sequence analysis. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448.
55. Raine A. R. C., Scrutton N. S., Mathews F. S. On the evolution of alternate core packing in eightfold (β/α)-barrels. Protein Sci. 3:1994;1889-1892.
56. Rao J. P., Grzemski W., Murphy P. J. Rhizobium melitoti lacking mosA synthesizes the rhizopine scyllo -inosamine in place of 3-o -methyl- scyllo -inosamine. Microbiology. 141:1995;1683-1690.
57. Reardon D., Farber G. K. The structure and function of α/β barrel proteins. FASEB J. 9:1995;497-503.
58. Richaud F. V., Richaud C., Ratet P., Patte J.-C. Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene. J. Bacteriol. 166:1986;297-300.
59. Roussel A., Cambillau C. Turbo-Frodo molecular modelling package. In Silicon Graphics Geometry Partner Directory. 1989;Silicon Graphics, Mountain View, CA.
60. Schauer R., Wember M. Inhibition of acylneuraminate pyruvate-lyase: evidence of intermediary Schiff's base formation and of a possible role of histidine residues. Hoppe-Seyler Z. Physiol. Chem. 352:1971;1517-1523.
61. Scrutton N. S. α/β Barrel evolution and the modular assembly of enzymes: emerging trends in the flavin oxidase/dehydrogenase family. BioEssays. 16:1994;115-122.
62. Silk G. W., Matthews B. F., Somers D. A., Gengenbach B. G. Cloning and expression of the soybean dapA gene encoding dihydrodipicolinate synthase. Plant Mol. Biol. 26:1994;989-993.
63. Teng T.-Y. Mounting of crystals for macromolecular crystallography in a free-standing thin film. J. Appl. Crystallog. 23:1990;387-391.
64. Varghese J. N., Colman P. M. Three-dimensional structure of the neuraminidase of influenza virus A/Tokyo/3/67 at 2.2 Å resolution. J. Mol. Biol. 221:1991;473-486.
65. Vauterin M., Jacobs M. Isolation of a poplar and an Arabidopsis thaliana dihydrodipicolinate synthase cDNA clone. Plant Mol. Biol. 25:1994;545-550.
66. Wilmanns M., Hyde C. C., Davies D. R., Kirschner K., Jansonius J. N. Structural conservation in parallel (β/α)-barrel enzymes that catalyse three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry. 30:1991;9161-9169.
67. Wilmot C. M., Thornton J. M. Analysis and prediction of the different types of β-turn in proteins. J. Mol. Biol. 203:1988;221-232.