New insights for dinucleotide backbone binding in conserved C5'-H...O hydrogen bonds

Journal of Molecular Biology

Volumn 279, Issue 4, 1998, Pages 695-701

  Chu, Pei Ying ^a   Hwang, Ming Jing ^a  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

Author keywords

C H...O hydrogen bonds; NAD; NADP; Phosphate backbone; Protein nucleotide recognition

Indexed keywords

DINUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

CHEMICAL STRUCTURE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW;

EID: 0032546730     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1822     Document Type: Article

References (17)

1. Baker, P. J., Britton, K. L., Rice, D. W., Rob, A. & Stillman, T. J. (1992). Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold. J. Mol. Biol. 228, 662-671.
2. Bella, J. & Helen, M. B. (1996). Crystallographic evidence for Cα-H...O=C hydrogen bonds in a collagen triple helix. J. Mol. Biol. 264, 734-742.
3. Bellamacina, C. R. (1996). The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins. FASEB J. 10, 1257-1269.
4. Carugo, O. & Argos, P. (1997a). NADP-dependent enzymes. I: conserved stereochemistry of cofactor binding. Proteins: Struct. Funct. Genet. 28, 10-28.
5. Carugo, O. & Argos, P. (1997b). NADP-dependent enzymes. II: evolution of the mono- and dinucleotide binding domains. Proteins: Struct. Funct. Genet. 28, 29-40.
6. Derewenda, Z. S., Derewenda, U. & Kobos, P. (1994). (His)Cε-H...O=C< hydrogen bond in the active sites of serine hydrolase. J. Mol. Biol. 241, 83-93.
7. Derewenda, Z. S., Lee, L. & Derewenda, U. (1995). The occurrence of C-H...O hydrogen bonds in proteins. J. Mol. Biol. 252, 248-262.
8. Desiraju, G. R. (1996). The C-H...O hydrogen bond: structural implications and supramolecular design. Acc. Chem. Res. 29, 441-449.
9. Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
10. Mayer-Jung, C., Moras, D. & Timsit, Y. (1997). Effect of cytosine methylation on DNA-DNA recognition at CpG steps. J. Mol. Biol. 270, 328-335.
11. Moodie, S. L. & Thornton, J. M. (1993). A study into the effects of protein binding on nucleotide conformation. Nucl. Acids Res. 21, 1369-1380.
12. Nyburg, S. C., Faerman, C. H. & Prasad, L. (1987). A revision of van der Waals atomic radii for molecular crystals. II: hydrogen bonded to carbon. Acta Crystallog. sect. B, 43, 106-110.
13. Rossman, M. G., Liljas, A., Bränden, C.-I. & Banaszak, L. J. (1975). Evolutionary and structural relationships among dehydrogenases. In The Enzymes (Boyer, P. D., ed.), 3rd edit. vol. 11, part A, pp. 61-102, Academic Press, New York.
14. Saenger, W. (1984). Principles of Nucleic Acid Structure, Springer-Verlag, Berlin, Germany.
15. Saraste, M., Sibbald, P. R. & Wittinghofer, A. (1990). The P-loop: a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15, 430-434.
16. Steiner, T. & Saenger, W. (1992). Geometry of C-H...O hydrogen bonds in carbohydrate crystal structures. Analysis of neutron diffraction data. J. Am. Chem. Soc. 114, 10146-10154.
17. Wahl, M. C. & Sundaralingam, M. (1997). C-H...O hydrogen bond in biology. Trends Biochem. Sci. 22, 97-102.