Divergent evolution of function in the ROK sugar kinase superfamily: Role of enzyme loops in substrate specificity

Biochemistry

Volumn 46, Issue 47, 2007, Pages 13564-13572

  Larion, Mioara ^a   Moore, Lauren B ^a   Thompson, Steven M ^a   Miller, Brian G ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE SUBSTITUTIONS; PHOSPHORYL TRANSFER ACTIVITY; SUBSTRATE SPECIFICITY; SUGAR KINASE;

ESCHERICHIA COLI; GENES; GLUCOSE; NUCLEOTIDES; SUBSTITUTION REACTIONS; SUGAR (SUCROSE);

ENZYMES;

ALLOKINASE; CARBOHYDRATE; GLUCOKINASE; N ACETYL DEXTRO MANNOSAMINE KINASE; PHOSPHOTRANSFERASE; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BACTERIAL KINETICS; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SPECIFICITY; GENE SEQUENCE; MATRIX ATTACHMENT REGION; MOLECULAR EVOLUTION; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN FUNCTION; REPRESSOR GENE; SUBSTITUTION REACTION;

AMINO ACID SEQUENCE; BINDING SITES; CATALYSIS; ENZYME STABILITY; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GLUCOKINASE; GLUCOSE; HEXOSAMINES; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN FOLDING; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI K12;

EID: 36749023905     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi700924d     Document Type: Article

References (44)

1. Taylor, S. V., Kast, P., and Hilvert, D. (2001) Investigating and engineering enzymes by genetic selection, Angew. Chem., Int. Ed. 40, 3310-3335.
2. Farinas, E. T., Butler, T., and Arnold, F. H. (2001) Directed enzyme evolution, Curr. Opin. Biotechnol. 12, 545-551.
3. Lutz, S., and Patrick, W. M. (2004) Novel methods for directed evolution of enzymes: Quality, not quantity, Curr. Opin. Biotechnol. 15, 291-297.
4. Kaur, J., and Sharma, R. (2006) Directed evolution: An approach to engineer enzymes, Crit. Rev. Biotechnol. 26, 165-199.
5. 8-Barrels: In vitro enhancement of a "new" reaction in the enolase superfamily, Biochemistry 44, 11722-11729.
6. Roodveldt, C., and Tawfik, D. S. (2005) Shared promiscuous activities and evolutionary features in various members of the amidohydrolase superfamily, Biochemistry 44, 12728-12736.
7. Miller, B. G., and Raines, R. T. (2004) Identifying latent enzyme activities: Substrate ambiguity within modern bacterial sugar kinases, Biochemistry 43, 6387-6392.
8. Miller, B. G., and Raines, R. T. (2005) Reconstitution of a defunct glycolytic pathway via recruitment of ambiguous sugar kinases, Biochemistry 44, 10776-10783.
9. Titgemeyer, F., Reizer, J., Reizer, A., and Saier, M. H. (1994) Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria, Microbiology 140, 2349-2354.
10. Holmes, K. C., Sander, C., and Valencia, A. (1993) A new ATP-binding fold in actin, hexokinase and Hsc70, Trends Cell Biol. 3, 53-59.
11. Patskovsky, Y., and Almo, S., (2005) Crystal structure of Escherichia coli putative N-acetyl-D-mannosamine kinase, New York Structural Genomics Consortium (to be published).
12. Brunzelle, J. S., Minasov, G., Shuvalova, L., Collart, F. R., and Anderson, W. F. (2005) Crystal structure of the putative regulatory protein, Midwest Center for Structural Genomics (to be published).
13. Schiefner, A., Gerber, K., Seitz, S., Weite, W., Diederichs, K., and Boos, W. (2005) The crystal structure of Mlc, a global regulator of sugar metabolism in Escherichia coli, J. Biol. Chem. 280, 29073-29079.
14. Mukai, T., Kawai, S., Mori, S., Mikami, B., and Murata, K. (2004) Crystal structure of bacterial inorganic polyphosphate/ATP-glucomannokinase, J. Biol. Chem. 279, 50591-50600.
15. Hofmann, K., Bucher, P., Falquet, L., and Bairoch, A. (1999) The PROSITE database, its status in 1999, Nucleic Acids Res. 27, 215-219.
16. Lunin, V. V., Li, Y., Schrag, J. D., Iannuzzi, P., Cygler, M., and Matte, A. (2004) Crystal structure of Escherichia coli ATP-dependent glucokinase and its complex with glucose, J. Bacteriol. 186, 6915-6927.
17. Kim, C., Song, S., and Park, C. (1997) The D-allose operon of Escherichia coli K-12, J. Bacteriol. 179, 7631-7637.
18. Poulsen, T., Chang, Y.-Y., and Hove-Jensen, B. (1999) D-Allose catabolism of Escherichia coli: Involvement of alsI and regulation of als regulon expression by allose and ribose, J. Bacteriol. 181, 7126-7130.
19. Plumbridge, J., and Vimr, E. (1999) Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuramic Acid by Escherichia coli, J. Bacteriol. 181, 47-54.
20. Ringenberg, M. A., Steenberg, S. M., and Vimr, E. R. (2003) The first committed step in the biosynthesis of sialic acid by Escherichia coli K1 does not involve a phosphorylated N-acetylmannosamine intermediate, Mol. Microbiol. 50, 961-975.
21. Uehara, T., and Park, J. T. (2004) The N-acetyl-D- glucosamine kinase of Escherichia coli and its role in murein recycling, J. Bacteriol. 186, 7273-7279.
22. Sproul, A. A., Lambourne, L. T. M., Jean-Jacques, D. J., and Kornberg, H. L. (2001) Genetic control of manno(fructo)kinase activity in Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 98, 15257-15259.
23. D'Souza, V. T., and Bender, M. L. (1987) Miniature organic models of enzymes, Acc. Chem. Res. 20, 146-152.
24. Fischer, E. (1894) Einfluss der configuration auf die Wirkung derenzyme, Ber. Dtsch. Chem. Ges. 27, 2985-2993.
25. Koshland, D. E., Jr. (1958) Application of a theory of enzyme specificity to protein synthesis, Proc. Natl. Acad. Sci. U.S.A. 44, 98-104.
26. Fersht, A. (1974) Catalysis, binding and enzyme-substrate complementarity, Proc. R. Soc. London, Ser. B 187, 397-407.
27. Herschlag, D. (1988) The role of induced fit and conformational changes of enzymes in specificity and catalysis, Bioorg. Chem. 16, 62-96.
28. Post, C. B., and Ray, W. J. (1995) Reexamination of induced fit as a determinant of substrate specificity in enzymatic reactions, Biochemistry 34, 15881-15885.
29. Hedstrom, L. (1996) Trypsin: A case study in the structural determinants of enzyme specificity, Biol. Chem. 377, 465-470.
30. Pasternak, A., White, A., Jeffery, J. C., Medina, N., Cahoon, M., Ringe, D., and Hedstrom, L. (2001) The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity, Protein Sci. 10, 1331-1342.
31. Tsai, Y.-C., and Johnson, A. K. (2006) A new paradigm for DNA polymerase specificity, Biochemistry 45, 9675-9687.
32. Matsumura, I., and Ellington, A. D. (2001) In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates, J. Mol. Biol. 305, 331-339.
33. Aharoni, A., Gaidukov, L., Khersonsky, O., McQ, G. S., Roodveldt, C., and Tawfik, D. S. (2005) The evolvability of promiscuous protein functions, Nat. Genet. 37, 73-76.
34. Slein, M. W. (1963) D-Glucose determinations with hexokinase and glucose 6-phosphate dehydrogenase, in Methods of Enzymatic Analysis (Bergmeyer, H. U., Ed.) Academic Press, San Diego, CA, p 117.
35. Easterby, J. S. (1973) Coupled enzyme assays: A general expression for the transient, Biochim. Biophys. Acta. 293, 552-558.
36. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice, Nucleic Acids Res. 22, 4673-4680.
37. Eddy, S. R. (1998) Profile hidden Markov models, Bioinformatics 14, 755-763.
38. Armougom, F., Moretti, S., Poirot, O., Audic, S., Dumas, P., Schaeli, B., Keduas, V., and Notredame, C. (2006) Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee, Nucleic Acids Res. 34, 604-608.
39. Gilbert, D. G. (1990-2006) ReadSeq(dDistributed by the author), Biology Department, Indiana University, Bloomington, IN. See http://iubio.bio.indiana. edu/soft/molbio/readseq/.
40. Felsenstein, J. (1980-2007) PHYLIP (Phylogeny Inference Package) version 3.6 (distributed by the author), Department of Genome Sciences, University of Washington, Seattle, WA. Available at http://evolution.genetics.washington.edu/ phylip.html.
41. Jones, D. T., Taylor, W. R. and Thornton, J. M. (1992) The rapid generation of mutation data matrices from protein sequences, Comput. Appl. Biosci. 8, 275-282.
42. Abascal, F., Zardoya, R., and Posada, D. (2005) ProtTest: Selection of best-fit models of protein evolution, Bioinformatics 21, 2104-2105.
43. Smith, S. W., Overbeek, R., Woese, C. R., Gilbert, W., and Gillevet, P. M. (1994) The Genetic Data Environment, an expandable GUI for multiple sequence analysis, Comput. Appl. Biosci. 10, 671-675.
44. Genetics Computer Group. (Copyright 1982-2007) Program Manual for the Wisconsin Package, version 11, Accelrys, Inc., San Diego, CA.