Conserved positions for ribose recognition: Importance of water bridging interactions among ATP, ADP and FAD-protein complexes

Journal of Molecular Biology

Volumn 323, Issue 3, 2002, Pages 523-532

  Babor, Mariana ^a   Sobolev, Vladimir ^a   Edelman, Marvin ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Consensus structure; Hydrogen bonding; Molecular recognition; Nucleotides; Protein ligand interactions

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; FLAVINE ADENINE NUCLEOTIDE; LIGAND; PROTEIN; RIBOSE; WATER;

ARTICLE; ATOMIC PARTICLE; CONFORMATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 0036408749     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00975-0     Document Type: Article

References (44)

1. Schulz, G. E. (1992). Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2, 61-67.
2. Moodie, S. L., Mitchell, J. B. & Thornton, J. M. (1996). Protein recognition of adenylate: An example of a fuzzy recognition template. J. Mol. Biol. 263, 486-500.
3. Traut, T. W. (1994). The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur. J. Biochem. 222, 9-19.
4. Kobayashi, N. & Go, N. (1997). A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition. Eur. Biophys. J. 26, 135-144.
5. Kobayashi, N. & Go, N. (1997). ATP binding proteins with different folds share a common ATP-binding structural motif. Nature Struct. Biol. 4, 6-7.
6. Denessiouk, K. A. & Johnson, M. S. (2000). When fold is not important: A common structural frame- work for adenine and AMP binding in 12 unrelated protein families. Proteins: Struct. Funct. Genet. 38, 310-326.
7. Denessiouk, K. A., Rantanen, V. V. & Johnson, M. S. (2001). Adenine recognition: A motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins: Struct. Funct. Genet. 44, 282-291.
8. Kinoshita, K., Sadanami, K., Kidera, A. & Go, N. (1999). Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of protein-mono-nucleotide complexes. Protein Eng. 12, 11-14.
9. Altona, C. & Sundaralingam, M. (1972). Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94, 8205-8212.
10. Saenger, W. (1984). Principles of Nucleic Acids Structure, Springer, New York.
11. Olson, W. & Sussman, J. L. (1982). How flexible is the furanose ring? A comparison of experimental and theoretical studies. J. Am. Chem. Soc. 104, 270-278.
12. Moodie, S. L. & Thornton, J. M. (1993). A study into the effects of protein binding on nucleotide conformation. Nucl. Acids Res. 21, 1369-1380.
13. Kuttner, Y. Y., Babor, M., Edelman, M. & Sobolev, V. (2001). Structural commonality in protein binding sites for ATP. In Currents in Computational Molecular Biology 2001 (El-Mabrouk, N., Lengauer, T. & Sankoff, D., eds), pp. 91-92, Les Publications CRM, Montreal.
14. Scrutton, N. S., Berry, A. & Perham, R. N. (1990). Redesign of the coenzyme specificity of a dehydrogenase by protein engineering. Nature, 343, 38-43.
15. Hurley, J. H., Chen, R. & Dean, A. M. (1996). Determinants of cofactor specificity in isocitrate dehydrogenase: Structure of an engineered NADP + → NAD + specificity-reversal mutant. Biochemistry, 35, 5670-5678.
16. Galkin, A., Kulakova, L., Ohshima, T., Esaki, N. & Soda, K. (1997). Construction of a new leucine dehydrogenase with preferred specificity for NADP + by site-directed mutagenesis of the strictly NAD + -specific enzyme. Protein Eng. 10, 687-690.
17. Pearl, F. M., Lee, D., Bray, J. E., Sillitoe, I., Todd, A. E., Harrison, A. P. et al. (2000). Assigning genomic sequences to CATH. Nucl. Acids Res. 28, 277-282.
18. Baker, E. N. & Hubbard, R. E. (1984). Hydrogen bonding in globular proteins. Progr. Biophys. Mol. Biol. 44, 97-179.
19. McDonald, I. K. & Thornton, J. M. (1994). Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777-793.
20. Bruns, C. M. & Karplus, P. A. (1995). Refined crystal structure of spinach ferredoxin reductase at 1.7 Åresolution: Oxidized, reduced and 2′-phospho-5′-AMP bound states. J. Mol. Biol. 247, 125-145.
21. Wierenga, R. K., De Maeyer, M. C. H. & Hol, W. G. J. (1985). Interaction of pyrophosphate moieties with α-helices in dinucleotide binding proteins. Biochemistry, 24, 1346-1357.
22. Wierenga, R. K., Terpstra, P. & Hol, W. G. (1986). Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol. 187, 101-107.
23. Rossmann, M. G., Liljas, A., Branden, C. I. & Banaszak, L. J. (1975). Evolutionary and structural relationships among dehydrogenases. In The Enzymes (Boyer, P. D., ed.), Academic Press, New York.
24. Ziegler, G. A., Vonrhein, C., Hanukoglu, I. & Schulz, G. E. (1999). The structure of adrenodoxin reductase of mitochondrial P450 systems: Electron transfer for steroid biosynthesis. J. Mol. Biol. 289, 981-990.
25. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
26. Galperin, M. Y. & Koonin, E. V. (1997). A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Protein Sci. 6, 2639-2643.
27. Janin, J. (1999). Wet and dry interfaces: The role of solvent in protein-protein and protein-DNA recognition. Struct. Fold. Des. 7, R277-R279.
28. Meyer, E. (1992). Internal water molecules and H-bonding in biological macromolecules: A review of structural features with functional implications. Protein Sci. 1, 1543-1562.
29. Williams, M. A., Goodfellow, J. M. & Thornton, J. M. (1994). Buried waters and internal cavities in monomeric proteins. Protein Sci. 3, 1224-1235.
30. Shakked, Z., Guzikevich-Guerstein, G., Frolow, F., Rabinovich, D., Joachimiak, A. & Sigler, P. B. (1994). Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature, 368, 469-473.
31. Schneider, B. & Berman, H. M. (1995). Hydration of the DNA bases is local. Biophys. J. 69, 2661-2669.
32. Reddy, C. K., Das, A. & Jayaram, B. (2001). Do water molecules mediate protein-DNA recognition? J. Mol. Biol. 314, 619-632.
33. Klebe, G. (1994). The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands. J. Mol. Biol. 237, 212-235.
34. Laskowski, R. A., Thornton, J. M., Humblet, C. & Singh, J. (1996). X-site: Use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J. Mol. Biol. 259, 175-201.
35. Verdonk, M. L., Cole, J. C. & Taylor, R. (1999). Super-Star: A knowledge-based approach for identifying interaction sites in proteins. J. Mol. Biol. 289, 1093-1108.
36. Rantanen, V.-V., Denessiouk, K. A., Gyllenberg, M., Koski, T. & Johnson, M. S. (2001). A fragment library based on gaussian mixtures predicting favorable molecular interactions. J. Mol. Biol. 313, 197-214.
37. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H. et al. (2000). The protein data bank. Nucl. Acids Res. 28, 235-242.
38. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Jr, Brice, M. D., Rodgers, J. R. et al. (1977). The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
39. Needleman, S. B. & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
40. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997). CATH-A hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
41. Senda, T., Yamada, T., Sakurai, N., Kubota, M., Nishizaki, T., Masai, E. et al. (2000). Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase. J. Mol. Biol. 304, 397-410.
42. Dobritzsch, D., Schneider, G., Schnackerz, K. D. & Lindqvist, Y. (2001). Crystal structure of dihydro-pyrimidine dehydrogenase, a major determinant of the pharmacokinetics of the anti-cancer drug 5-fluorouracil. EMBO J. 20, 650-660.
43. Sobolev, V., Sorokine, A., Prilusky, J., Abola, E. E. & Edelman, M. (1999). Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332.
44. Thanki, N., Thornton, J. M. & Goodfellow, J. M. (1988). Distributions of water around amino acid residues in proteins. J. Mol. Biol. 202, 637-657.