Structural similarities between thiamin-binding protein and thiaminase-I suggest a common ancestor

Biochemistry

Volumn 47, Issue 5, 2008, Pages 1346-1357

  Soriano, Erika V ^a   Rajashankar, Kanagalaghatta R ^a   Hanes, Jeremiah W ^a   Bale, Shridhar ^a   Begley, Tadhg P ^a   Ealick, Steven E ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PERIPLASMIC BINDING PROTEINS; PROKARYOTIC CELLS; THIAMIN PYROPHOSPHATE;

BACTERIA; BINDING SITES; CELL MEMBRANES; CRYSTAL STRUCTURE; DISSOCIATION; SOLUBILITY;

ENZYME KINETICS;

ABC TRANSPORTER; BINDING PROTEIN; ENZYME; PHOSPHATE; PYROPHOSPHATE; THIAMINASE 1; THIAMINE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BINDING SITE; CRYSTAL STRUCTURE; CYTOPLASM; DISSOCIATION CONSTANT; ESCHERICHIA COLI; GRAM NEGATIVE BACTERIUM; MEASUREMENT; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROKARYOTIC CELL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; SALMONELLA TYPHIMURIUM; TBPA GENE;

ALKYL AND ARYL TRANSFERASES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; KINETICS; MODELS, MOLECULAR; THIAMINE; THIAMINE PYROPHOSPHATE;

ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA; SALMONELLA TYPHIMURIUM;

EID: 38849178185     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7018282     Document Type: Article

References (55)

1. Harper, C. (2006) Thiamine (vitamin B1) deficiency and associated brain damage is still common throughout the world and prevention is simple and safe! Eur. J. Neurol. 13, 1078-1082.
2. Begley, T. P., Downs, D. M., Ealick, S. E., McLafferty, F. W., Van Loon, A. P., Taylor, S., Campobasso, N., Chiu, H. J., Kinsland, C., Reddick, J. J., and Xi, J. (1999) Thiamin biosynthesis in prokaryotes, Arch. Microbiol. 171, 293-300.
3. Godoi, P. H., Galhardo, R. S., Luche, D. D., Van Sluys, M. A., Menck, C. F., and Oliva, G. (2006) Structure of the thiazole biosynthetic enzyme THI1 from Arabidopsis thaliana, J. Biol. Chem. 281, 30957-30966.
4. Chatterjee, A., Jurgenson, C. T., Schroeder, F. C., Ealick, S. E., and Begley, T. P. (2006) Thiamin biosynthesis in eukaryotes: characterization of the enzyme-bound product of thiazole synthase from Saccharomyces cerevisiae and its implications in thiazole biosynthesis, J. Am. Chem. Soc. 128, 7158-7159.
5. Jurgenson, C. T., Chatterjee, A., Begley, T. P., and Ealick, S. E. (2006) Structural insights into the function of the thiamin biosynthetic enzyme Thi4 from Saccharomyces cerevisiae, Biochemistry 45, 11061-11070.
6. Jones, P. M., and George, A. M. (2004) The ABC transporter structure and mechanism: perspectives on recent research, Cell. Mol Life Sci. 61, 682-699.
7. Davidson, A. L., and Chen, J. (2004) ATP-binding cassette transporters in bacteria, Annu. Rev. Biochem. 73, 241-268.
8. Hollenbach, A. D., Dickson, K. A., and Washabaugh, M. W. (2002) Overexpression, purification, and characterization of the periplasmic space thiamin-binding protein of the thiamin traffic ATPase in Escherichia coli, Protein Expression Purif. 25, 508-518.
9. Webb, E., Claas, K., and Downs, D. (1998) thiBPQ encodes an ABC transporter required for transport of thiamine and thiamine pyrophosphate in Salmonella typhimurium, J. Biol. Chem. 273, 8946-8950.
10. Campobasso, N., Costello, C. A., Kinsland, C., Begley, T. P., and Ealick, S. E. (1998) Crystal structure of thiaminase-I from Bacillus thiaminolyticus at 2.0 Å resolution, Biochemistry 37, 15981-15989.
11. 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.
12. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. 276, 307-326.
13. Matthews, B. W. (1968) Solvent content of protein crystals, J. Mol. Biol. 33, 491-497.
14. Schneider, T. R., and Sheldrick, G. M. (2002) Substructure solution with SHELXD, Acta Crystallogr, Sect. D 58, 1772-1779.
15. Collaborative Computational Project-Number 4. (1994) The CCP-4 suite: programs for protein crystallography, Acta Crystallogr., Sect. D 50, 760-763.
16. Terwilliger, T. C., and Berendzen, J. (1999) Automated MAD and MIR structure solution, Acta Crystallogr., Sect. D 55, 849-861.
17. Emsley, P., and Cowtan, K. (2004) Coot: model-building tools for molecular graphics, Acta Crystallogr., Sect. D 60, 2126-2132.
18. Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S., and Dodson, E. J. (1999) Efficient anisotropic refinement of macromolecular structures using FFT, Acta Crystallogr., Sect. D 55, 247-255.
19. 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, Sect. D 54, 905-921.
20. Kleygert, G. J., and Jones, T. A. (1996) xdlMAPMAN and xdlDATAMAN-programs for reformatting, analysis, and manipulation of biomacromolecular electron-density maps and reflection datasets, Acta Crystallogr., Sect. D 52, 826-828.
21. Kleywegt, G. J., and Jones, T. A. (1997) Template convolution to enhance or detect structural features in macromolecular electron-density maps, Acta Crystallogr., Sect. D 53, 179-185.
22. Johnson, K. A. (2003) in Introduction to kinetic analysis of enzyme systems, in Kinetic Analysis of Macromolecules (Johnson, K. A., Ed.) pp 1-17, Oxford University Press, New York.
23. Mohamadi, F., Richards, N. G. J., Guida, W. C., Liskamp, R., Lipton, M., Caufield, C., Chang, G., Hendrickson, T., and Still, W. C. (1990) MacroModel - an integrated software system for modeling organic and bioorganic molecules using molecular mechanics, J. Comput. Chem. 11, 460-467.
24. Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., Jr., and Weiner, P. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins, J. Am. Chem. Soc. 106, 765-784.
25. Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A. (1986) An all atom force field for simulations of proteins and nucleic acids, J. Comput. Chem. 7, 230-252.
26. Ponder, J. W., and Richards, F. M. (1987) An efficient Newton-like method for molecular mechanics energy minimization of large molecules, J. Comput. Chem. 8, 1016-1024.
27. Esnouf, R. (1997) An extensively modified version of Molscript which includes greatly enhanced colouring capabilities, J. Mol. Graphics 15, 132-134.
28. Esnouf, R. M. (1999) Further additions to MolScript version 1.4, including reading and contouring of electron-density maps, Acta Crystallogr., Sect. D 55, 938-940.
29. Merritt, E. A., and Bacon, D. J. (1997) Raster3D: Photorealistic Molecular Graphics, Methods Enzymol. 277, 505-524.
30. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA.
31. Nossal, N. G., and Heppel, L. A. (1966) The release of enzymes by osmotic shock from Escherichia coli in exponential phase, J. Biol. Chem. 241, 3055-3062.
32. Tam, R., and Saier, M. H., Jr. (1993) Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria, Microbiol. Rev. 57, 320-346.
33. Quiocho, F. A., and Ledvina, P. S. (1996) Atomic structure and specificity of bacterial periplasmic receptors for active transport and Chemotaxis: variation of common themes, Mol. Microbiol. 20, 17-25.
34. Felder, C. B., Graul, R. C., Lee, A. Y., Merkle, H. P., and Sadee, W. (1999) The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors, AAPS PharmSci 1, E2.
35. Fukami-Kobayashi, K., Tateno, Y., and Nishikawa, K. (1999) Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history, J. Mol. Biol. 286, 279-290.
36. Spurlino, J. C., Lu, G. Y., and Quiocho, F. A. (1991) The 2.3 Å resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis, J. Biol. Chem. 266, 5202-5219.
37. Mao, B., Pear, M. R., McCammon, J. A., and Quiocho, F. A. (1982) Hinge-bending in L-arabinose-binding protein. The "Venus's- flytrap" model, J. Biol Chem. 257, 1131-1133.
38. Sack, J. S., Saper, M. A., and Quiocho, F. A. (1989) Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine, J. Mol. Biol. 206, 171-191.
39. Acher, F. C., and Bertrand, H. O. (2005) Amino acid recognition by Venus flytrap domains is encoded in an 8-residue motif, Biopolymers 80, 357-366.
40. Duan, X., and Quiocho, F. A. (2002) Structural evidence for a dominant role of nonpolar interactions in the binding of a transport/chemosensory receptor to its highly polar ligands, Biochemistry 41, 706-712.
41. Kandt, C., Xu, Z., and Tieleman, D. P. (2006) Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF, Biochemistry 45, 13284-13292.
42. Holm, L., and Sander, C. (1993) Protein structure comparison by alignment of distance matrices, J. Mol. Biol. 233, 123-138.
43. 3+-binding protein reveals convergent evolution within a superfamily, Nat. Struct. Biol. 4, 919-924.
44. Sugiyama, S., Vassylyev, D. G., Matsushima, M., Kashiwagi, K., Igarashi, K., and Morikawa, K. (1996) Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli, J. Biol. Chem. 271, 9519-9525.
45. Madej, T., Gibrat, J. F., and Bryant, S. H. (1995) Threading a database of protein cores, Proteins 23, 356-369.
46. Gibrat, J. F., Madej, T., and Bryant, S. H. (1996) Surprising similarities in structure comparison, Curr. Opin. Struct. Biol. 6, 377-385.
47. Devedjiev, Y., Surendranath, Y., Derewenda, U., Gabrys, A., Cooper, D. R., Zhang, R. G., Lezondra, L., Joachimiak, A., and Derewenda, Z. S. (2004) The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins, J. Mol. Biol. 343, 395-406.
48. Pletcher, J., Sax, M., Blank, G., and Wood, M. (1977) Stereochemistry of intermediates in thiamine catalysis. 2. Crystal structure of DL-2-(α-hydroxybenzyl)thiamine chloride hydrochloride trihydrate, J. Am. Chem. Soc. 99, 1396-1403.
49. 2O, Acta Crystallogr., Sect. B32, 2970-2975.
50. Chiu, H. J., Reddick, J. J., Begley, T. P., and Ealick, S. E. (1999) Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 Å resolution, Biochemistry 38, 6460-6470.
51. Timm, D. E., Liu, J., Baker, L. J., and Harris, R. A. (2001) Crystal structure of thiamin pyrophosphokinase, J. Mol. Biol. 310, 195-204.
52. Hawkins, C. F., Borges, A., and Perham, R. N. (1989) A common structural motif in thiamin pyrophosphate-binding enzymes, FEBS Lett. 255, 77-82.
53. Muller, Y. A., Lindqvist, Y., Furey, W., Schulz, G. E., Jordan, F., and Schneider, G. (1993) A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase, Structure 1, 95-103.
54. Nikkola, M., Lindqvist, Y., and Schneider, G. (1994) Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 Å resolution, J. Mol. Biol. 238, 387-404.
55. Jenkins, A. H., Schyns, G., Potot, S., Sun, G., and Begley, T. P. (2007) A new thiamin salvage pathway, Nat. Chem. Biol. 3, 492-497.