Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II

Biochemistry

Volumn 44, Issue 7, 2005, Pages 2319-2329

  Toms, Angela V ^a   Haas, Amy L ^a   Park, Joo Heon ^a   Begley, Tadhg P ^a   Ealick, Steven E ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; BACTERIA; CATALYSIS; CHARACTERIZATION; COMPLEXATION; GENES;

ENZYMATIC FUNCTIONS; EXTRACELLULAR PROTEASES; REGULATORY PROTEINS; STRUCTURAL CHARACTERIZATION;

PROTEINS;

4 AMINO 2 METHYL 5 HYDROXYMETHYLPYRIMIDINE; ASPARTIC ACID; CYSTEINE; GENE PRODUCT; GLUTAMINE; GLYCINE; LEUCINE; PROTEIN; PROTEIN TENA; PROTEIN TENI; PYRIMIDINE DERIVATIVE; SYNTHETASE; THIAMINASE II; THIAMINE PHOSPHATE; THIAMINE PHOSPHATE SYNTHASE; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; CATALYSIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ALKYL AND ARYL TRANSFERASES; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; HYDROLASES; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PYRIMIDINES; REPRESSOR PROTEINS; SULFATES; THIAMINE TRIPHOSPHATE; TRANS-ACTIVATORS;

EID: 14044270800     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0478648     Document Type: Article

References (36)

1. Settembre, E., Begley, T. P., and Ealick, S. E. (2003) Structural biology of enzymes of the thiamin biosynthesis pathway, Curr. Opin. Struct. Biol. 13, 739-747.
2. Lee, J.-M., Zhang, S., Sana, S., Santa Anna, S., Jiang, C., and Perkins, J. (2001) RNA expression analysis using an antisense Bacillus subtilis genome array, J. Bacteriol. 183, 7371-7380.
3. Pang, A. S. H., Nathoo, S., and Wong, S. L. (1991) Cloning and characterization of a pair of novel genes that regulate production of extracellular enzymes in Bacillus subtilis, J. Bacteriol. 173, 46-54.
4. Strauch, M. A. (1993) Regulation of Bacillus subtilis gene expression during the transition from exponential growth to stationary phase, Prog. Nucleic Add Res. Mol. Biol. 46, 121-53.
5. Rodionov, D. A., Vitreschak, A. G., Mironov, A. A., and Gelfand, M. S. (2002) Comparative Genomics of Thiamin Biosynthesis in Procaryotes. New genes and regulatory mechanisms, J. Biol. Chem. 277, 48949-48959.
6. Chiu, H., Reddick, J., Begley, T., and Ealick, S. (1999) Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 Å resolution, Biochemistry 38, 6460-6470.
7. 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, 248-54.
8. Jancarik, J., and Kim, S. H. (1991) Sparse-Matrix Sampling-a Screening Method for Crystallization of Proteins, J. Appl. Crystallogr. 24, 409-411.
9. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
10. Itou, H., Yao, M., Watanabe, N., and Tanaka, I. (2004) Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii, Acta Crystallogr. D 60, 1094-1100.
11. Sali, A., and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol. 234, 779-815.
12. Marti-Renom, M. A., Yerkovich, B., and Sali, A. (2002) Comparative protein structure prediction, Wiley, New York.
13. Vagin, A., and Teplyakov, A. (2000) An approach to multi-copy search in molecular replacement, Acta Crystallogr. D 56, 1622-4.
14. Collaborative Computational Project Number 4. (1994) The CCP-4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
15. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for the building of protein models in electron density maps and the location of errors in these models, Acta Crystallogr. A 47, 110-119.
16. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D 54, 905-21.
17. Esnouf, R. (1997) An extensively modified version of Molscript which includes greatly enhanced colouring capabilities, J. Mol. Graphics 15, 132-134.
18. Esnouf, R. M. (1999) Further additions to MolScript version 1.4, inciuding reading and contouring of electron-density maps, Acta Crystallogr. D 55, 938-40.
19. Merritt, E. A. and Bacon, D. J. (1997) Raster3D: Photorealistic Molecular Graphics, Methods Enzymol. 277, 505-524.
20. Christopher, J. A. (1998) SPOCK, Texas A&M University, College Station, TX.
21. Miller, R., DeTitta, G. T., Jones, R., Langs, D. A., Weeks, C. M., and Hauptman, H. A. (1993) On the application of the minimal principle to solve unknown structures, Science 259, 1430-3.
22. Miller, R., Gallo, S. M., Khalak, H. G., and Weeks, C. M. (1994) SnB: crystal structure determination via shake-and-bake, J. Appl. Crystallogr. 27, 613-21.
23. Smith, G. D., Nagar, B., Rini, J. M., Hauptman, H. A., and Blessing, R. H. (1998) The use of SnB to determine an anomalous scattering substructure, Acta Crystallogr. D 54, 799-804.
24. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
25. Ramakrishnan, C. and Ramachandran, G. N. (1965) Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units, Biophys. J. 5, 909-33.
26. Holm, L., and Sander, C. (1993) Protein structure comparison by alignment of distance matrixes, J. Mol. Biol. 233, 123-38.
27. Evans, W. C. (1975) Thiaminases and their effects on animals, Vitam. Horm. 33, 467-504.
28. Fujita, A. (1954) Thiaminase, Adv. Enzymol. 15, 389-421.
29. Costello, C. A., Kelleher, N. L., Abe, M., McLafferty, F. W., and Begley, T. P. (1996) Mechanistic studies on thiaminase I. Overexpression and identification of the active site nucleophile, J. Biol. Chem. 271, 3445-52.
30. Campobasso, N., Costello, C., Kinsland, C., and Begley, T. P. (1998) Crystal structure of thiaminase I from Bacillus thiaminolyticus at 2.0 A resolution, Biochemistry 37, 15891-15989.
31. Lienhard, G. E. (1970) Kinetic evidence for a (4-amino-2-methyl-5- pyrimidinyl)methyl-enzyme intermediate in the thiaminase I reaction, Biochemistry 9, 3011-20.
32. Nicewonger, R., Costello, C. A., and Begley, T. P. (1996) Mechanistic Studies on Thiaminase I. 3. Stereochemistry of the Thiaminase I and the Bisulfite-Catalyzed Degradation of Chiral Monodeuteriothiamin, J. Org. Chem. 61, 4172-4174.
33. Zoltewicz, J. A., Uray, G., and Kauffman, G. M. (1980) Evidence for an Intermediate in Nucleophilic-Substitution of a Thiamin Analogue-Change from 1st-Order to 2nd-Order Kinetics in Sulfite Ion, J. Am. Chem. Soc. 102, 3653-3654.
34. 2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel, Biochemistry 37, 6247-55.
35. Peapus, D., Chiu, H.-J., Campobasso, N., Reddick, J., Begley, T., and Ealick, S. (2001) Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase, Biochemistry 40, 10103-10114.
36. Fisher, J. P., Fitzsimons, J. D., Combs, G. F., Jr., and Spitsbergen, J. M. (1996) Naturally occurring thiamine deficiency causing reproductive failure in finger lakes atlantic salmon and great lakes lake trout, Trans. Am. Fish. Soc. 125, 167-78.