Distinct roles of the active-site Mg2+ ligands, Asp 882 and Asp705, of DNA polymerase I (Klenow fragment) during the prechemistry conformational transitions

Journal of Biological Chemistry

Volumn 286, Issue 5, 2011, Pages 3755-3766

  Bermek, Oya ^a   Grindley, Nigel D F ^a   Joyce, Catherine M ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2-AMINOPURINE; ACTIVE SITE; ANCHOR POINT; ASPARTATES; CARBOXYLATE LIGANDS; CONFORMATIONAL TRANSITIONS; DNA CHAINS; DNA POLYMERASE; FLUORESCENCE ASSAY; KLENOW FRAGMENT; POLYMERASE ACTIVITIES; SIDE CHAINS; SITE GEOMETRY; STOPPED FLOW; TERNARY COMPLEX;

CARBOXYLATION; CATALYSIS; DNA; METAL IONS; NUCLEIC ACIDS; NUCLEOTIDES; POLYMERS;

LIGANDS;

2 AMINOPURINE; ASPARTIC ACID; ASPARTIC ACID 705; ASPARTIC ACID 882; CARBOXYLIC ACID; DNA DIRECTED DNA POLYMERASE BETA; MAGNESIUM ION; UNCLASSIFIED DRUG; LIGAND; MAGNESIUM;

AMINO ACID COMPOSITION; ARTICLE; CATALYSIS; CATION TRANSPORT; CONCENTRATION PROCESS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CHEMISTRY; ENZYME CONFORMATION; LIGAND BINDING; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; CHEMISTRY; METABOLISM; PHASE TRANSITION; PHYSIOLOGY; PROTEIN CONFORMATION;

ASPARTIC ACID; CATALYSIS; CATALYTIC DOMAIN; DNA POLYMERASE I; LIGANDS; MAGNESIUM; PHASE TRANSITION; PROTEIN CONFORMATION;

EID: 79952759975     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M110.167593     Document Type: Article

References (37)

1. Joyce, C. M., and Benkovic, S. J. (2004) Biochemistry 43, 14317-14324
2. Purohit, V., Grindley, N. D. F., and Joyce, C. M. (2003) Biochemistry 42, 10200-10211
3. Joyce, C. M., Potapova, O., Delucia, A. M., Huang, X., Basu, V. P., and Grindley, N. D. F. (2008) Biochemistry 47, 6103-6116
4. Doublié, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998) Nature 391, 251-258
5. Li, Y., Korolev, S., and Waksman, G. (1998) EMBO J. 17, 7514-7525
6. Johnson, S. J., Taylor, J. S., and Beese, L. S. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 3895-3900
7. Doublié, S., Sawaya, M. R., and Ellenberger, T. (1999) Structure 7, R31-R35
8. Brautigam, C. A., and Steitz, T. A. (1998) Curr. Opin. Struct. Biol. 8, 54-63
9. Dahlberg, M. E., and Benkovic, S. J. (1991) Biochemistry 30, 4835-4843
10. Zhong, X., Patel, S. S., and Tsai, M.-D. (1998) J. Am. Chem. Soc. 120, 235-236
11. Arndt, J. W., Gong, W., Zhong, X., Showalter, A. K., Liu, J., Dunlap, C. A., Lin, Z., Paxson, C., Tsai, M.-D., and Chan, M. K. (2001) Biochemistry 40, 5368-5375
12. Bakhtina, M., Lee, S., Wang, Y., Dunlap, C., Lamarche, B., and Tsai, M.-D. (2005) Biochemistry 44, 5177-5187
13. Wang, M., Lee, H. R., and Konigsberg, W. (2009) Biochemistry 48, 2075-2086
14. Delarue, M., Poch, O., Tordo, N., Moras, D., and Argos, P. (1990) Protein Eng. 3, 461-467
15. Steitz, T. A., Smerdon, S. J., Jäger, J., and Joyce, C. M. (1994) Science 266, 2022-2025
16. Polesky, A. H., Steitz, T. A., Grindley, N. D. F., and Joyce, C. M. (1990) J. Biol. Chem. 265, 14579-14591
17. Polesky, A. H., Dahlberg, M. E., Benkovic, S. J., Grindley, N. D. F., and Joyce, C. M. (1992) J. Biol. Chem. 267, 8417-8428
18. Joyce, C. M., and Derbyshire, V. (1995) Methods Enzymol. 262, 3-13
19. Li, Y., Kong, Y., Korolev, S., and Waksman, G. (1998) Protein Sci. 7, 1116-1123
20. Beese, L. S., Friedman, J. M., and Steitz, T. A. (1993) Biochemistry 32, 14095-14101
21. Astatke, M., Grindley, N. D. F., and Joyce, C. M. (1995) J. Biol. Chem. 270, 1945-1954
22. Mullen, G. P., Serpersu, E. H., Ferrin, L. J., Loeb, L. A., and Mildvan, A. S. (1990) J. Biol. Chem. 265, 14327-14334
23. Kiefer, J. R., Mao, C., Braman, J. C., and Beese, L. S. (1998) Nature 391, 304-307
24. Santoso, Y., Joyce, C. M., Potapova, O., Le Reste, L., Hohlbein, J., Torella, J. P., Grindley, N. D. F., and Kapanidis, A. N. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 715-720
25. Zakharova, E., Wang, J., and Konigsberg, W. (2004) Biochemistry 43, 6587-6595
26. Sarafianos, S. G., Clark, A. D., Jr., Das, K., Tuske, S., Birktoft, J. J., Ilankumaran, P., Ramesha, A. R., Sayer, J. M., Jerina, D. M., Boyer, P. L., Hughes, S. H., and Arnold, E. (2002) EMBO J. 21, 6614-6624
27. Batra, V. K., Beard, W. A., Shock, D. D., Krahn, J. M., Pedersen, L. C., and Wilson, S. H. (2006) Structure 14, 757-766
28. Radhakrishnan, R., Arora, K., Wang, Y., Beard, W. A., Wilson, S. H., and Schlick, T. (2006) Biochemistry 45, 15142-15156
29. Yang, W., Lee, J. Y., and Nowotny, M. (2006) Mol. Cell 22, 5-13
30. Cowan, J. A. (1998) Chem. Rev. 98, 1067-1088
31. Yang, L., Arora, K., Beard, W. A., Wilson, S. H., and Schlick, T. (2004) J. Am. Chem. Soc. 126, 8441-8453
32. Lee, H. R., Wang, M., and Konigsberg, W. (2009) Biochemistry 48, 2087-2098
33. Florián, J., Goodman, M. F., and Warshel, A. (2003) J. Am. Chem. Soc. 125, 8163-8177
34. Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., and Kraut, J. (1996) Biochemistry 35, 12762-12777
35. Kunkel, T. A., and Loeb, L. A. (1979) J. Biol. Chem. 254, 5718-5725
36. El-Deiry, W. S., Downey, K. M., and So, A. G. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 7378-7382
37. Goodman, M. F., Keener, S., Guidotti, S., and Branscomb, E. W. (1983) J. Biol. Chem. 258, 3469-3475