YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology

Biochemistry

Volumn 43, Issue 49, 2004, Pages 15472-15479

  Rajan, Shyamala S ^a   Yang, Xiaojing ^a   Shuvalova, Ludmilla ^a   Collart, Frank ^b   Anderson, Wayne F ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CHEMICAL BONDS; CRYSTAL STRUCTURE; DIMERS; PROTEINS; STOICHIOMETRY;

GRAM POSITIVE BACTERIA; METALLOPROTEASES; YFIT;

POLYPEPTIDES;

BACTERIAL PROTEIN; HISTIDINE; HYDROLASE; METALLOPROTEINASE; NICKEL; POLYPEPTIDE; PROTEIN YFIT; RECOMBINANT PROTEIN; THERMOLYSIN; UNCLASSIFIED DRUG; WATER;

ARTICLE; BACILLUS SUBTILIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; GEOMETRY; GRAM POSITIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STOICHIOMETRY; STRUCTURE ANALYSIS;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; GENOME, BACTERIAL; HYDROLASES; METALLOPROTEINS; NICKEL; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN; THERMOLYSIN;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); POSIBACTERIA;

EID: 10644264403     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048665r     Document Type: Article

References (31)

1. Whisstock, J. C., and Lesk, A. M. (2003) Prediction of protein function from protein sequence and structure, Q. Rev. Biophys. 36, 307-340.
2. Jones, S., and Thornton, J. M. (2004) Searching for functional sites in protein structures, Curr. Opin. Chem. Biol. 8, 3-7.
3. 2+-dependent phospho-α-glucosidase from Bacillus subtilis, Structure 12, 1619-1629.
4. Stols, L, Gu, M., Dieckman, L., Raffen, R., Collart, F. R., and Donnelly, M. I. (2002) A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site, Protein Expression Purif. 25, 8-15.
5. Leslie, A. G. W. (1992) Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB, Newsletter on Protein Crystallography 26.
6. Bailey, S. (1994) The CCP4 Suite: Programs for protein crystallography, Acta Crystallogr., Sect. D 50, 760-763.
7. Terwilliger, T. C., and Berendzen, J. (1999) Automated MAD and MIR structure solution, Acta Crystallogr., Sect. D 55, 849-861.
8. McRee, D. E. (1999) XtalView/Xfit - A versatile program for manipulating atomic coordinates and electron density, J. Struct. Biol. 125, 156-165.
9. Brunger, A. T. (1992) The Free R value: A novel statistical quantity for assessing the accuracy of crystal structures, Nature 355, 472-474.
10. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr., Sect. D 53, 240-255.
11. Holm, L., and Sander, C. (1993) Protein structure comparison by alignment of distance matrices, J. Mol. Biol. 233, 123-138.
12. Breiter, D. R., Kanost, M. R., Benning, M. M., Wesenberg, G., Law, J. H., Wells, M. A., Rayment, I., and Holden, H. M. (1991) Molecular structure of an apolipoprotein determined at 2.5 Å resolution, Biochemistry 30, 603-608.
13. Friedrich, R., Panizzi, P., Fuentes-Prior, P., Richter, K., Verhamme, I., Anderson, P. J., Kawabata, S., Huber, R., Bode, W., and Bock, P. E. (2003) Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation, Nature 425, 535-539.
14. Knowlton, J. R., Johnston, S. C, Whitby, F. G., Realini, C., Zhang, Z., Rechsteiner, M., and Hill, C. P. (1997) Structure of the proteasome activator REGα (PA28α), Nature 390, 639-643.
15. Senda, T., Shimazu, T., Matsuda, S., Kawano, G., Shimizu, H., Nakamura, K. T., and Mitsui, Y. (1992) Three-dimensional crystal structure of recombinant murine interferon-β, EMBO J. 11, 3193-3201.
16. Newville, M. (2003) Fundamentals of XAFS at http://cars9.uchicago.edu/ xafs/.
17. Tronrud, D. E., Monzingo, A. F., and Matthews, B. W. (1986) Crystallographic structural analysis of phosphoramidates as inhibitors and transition-state analogs of thermolysin, Eur. J. Biochem. 157, 261-268.
18. Calero, G., Gupta, P., Nonato, M. C., Tandel, S., Biehl, E. R., Hofmann, S. L., and Clardy, J. (2003) The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2, J. Biol. Chem. 278, 37957-37964.
19. Watt, R. K., and Ludden, P. W. (1999) Nickel-binding proteins. Cell. Mol. Life Sci. 56, 604-625.
20. Harding, M. M. (2001) Geometry of metal-ligand interactions in proteins, Acta Crystallogr., Sect. D 57, 401-411.
21. Gong, W., Zhu, X., Liu, S., Teng, M., and Niu, L. (1998) Crystal structures of Acutolysin A, a three-disulfide hemorrhagic zinc metalloproteinase from the snake venom of Agkistrodon acutus, J. Mol. Biol. 283, 657-668.
22. Brandstetter, H., Engh, R. A., Von Roedern, E. G., Moroder, L., Huber, R., Bode, W. and Grams, F. (1998) Structure of malonic acid-based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data, Protein Sci. 7, 1303-1309.
23. Chakravarty, S., Yadava, V. S., Kumar, V., and Kannan, K. K. (1985) Drug-protein interaction at the molecular level - A study of sulfonamide carbonic-anhydrase complexes, J. Biosci. 8, 491.
24. Karpusas, M., Nolte, M., Benton, C. B., Meier, W., Lipscomb, W. N., and Goelz, S. (1997) The crystal structure of human interferon β at 2.2 Å resolution, Proc. Natl. Acad. Sci. U.S.A. 94, 11813-11818.
25. Kester, W. R., and Matthews, B. W. (1977) Crystallographic study of the binding of dipeptide inhibitors to thermolysin: Implications for the mechanism of catalysis, Biochemistry 16, 2506-2516.
26. Anderson, W. F., Boodhoo, A., and Mol, C. D. (1988) The importance of purity in the crystallization of DNA binding immunoglobulin Fab fragments, J. Cryst. Growth 90, 153-159.
27. Corpet, F. (1998) Multiple sequence alignment with hierarchical clustering, Nucleic Acids Res. 16, 10881-10890.
28. Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) ESPript: Analysis of multiple sequence alignments in PostScript, Bioinformatics 15, 305-308.
29. Kraulis, P. J. (1991) MOLSCRIPT - A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
30. Merritt, E. A., and Bacon, D. J. (1997) Raster3D: Photorealistic molecular graphics, Methods Enzymol. 277, 505-524.
31. Esnouf, R. M. (1997) An extensively modified version of MolScript that includes generally enhanced coloring capabilities, J. Mol. Graphics Modell. 15, 132-134.