Structure of the adenylation domain of an NAD+-dependent DNA ligase

Structure

Volumn 7, Issue 1, 1999, Pages 35-42

  Singleton, Martin R ^a   Håkansson, Kjell ^a   Timson, David J ^a   Wigley, Dale B ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Antibiotics; DNA ligase; Protein structure

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

ADENYLATION; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME MECHANISM; ENZYME STRUCTURE; GEOBACILLUS STEAROTHERMOPHILUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING;

BACILLUS STEAROTHERMOPHILUS;

EID: 0033555464     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80007-0     Document Type: Article

References (23)

1. Lehman, I.R. (1974). DNA ligase: Structure, mechanism and function. Science 186, 790-797.
2. Lindahl, T. & Barnes, D.E. (1992). Mammalian DNA ligases. Annu. Rev. Biochem. 61, 251-281.
3. Shuman, S. & Schwer, B. (1995). RNA capping enzyme and DNA ligase: A superfamily of covalent nucleotidyl transferases. Mol. Microbiol. 17, 405-410.
4. Subramanya, H.S., Doherty, A.J., Ashford, S.R. & Wigley, D.B. (1996). Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85, 607-615.
5. Barany, F. (1991). Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl Acad. Sci. USA 88, 189-193.
6. Doherty, A.J. & Wigley, D.B. (1999). Functional domains of an ATP-dependent DNA ligase. J. Mol. Biol. 285, 63-71.
7. +-dependent DNA ligase. J. Mol. Biol. 285, 73-83.
8. Håkansson, K., Doherty, A.J., Shuman, S. & Wigley, D.B. (1997). X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell 89, 545-553.
9. Murzin, A.G. (1996). Structural classification of proteins: New superfamilies. Curr. Opin. Struct. Biol. 6, 386-394.
10. Doherty, A.J., Ashford, S.R. & Wigley, D.B. (1996). Characterisation of proteolytic fragments of bacteriophage T7 DNA ligase. Nucleic Acids Res. 24, 2281-2287.
11. Nicholls, A. & Honig, B.J. (1991). A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem. 12, 435-445.
12. Håkansson, K. & Wigley, D.B. (1998). Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping. Proc. Natl Acad. Sci. USA 95, 1505-1510.
13. Luo, J. & Barany, F. (1996). Identification of essential residues in Thermus thermophilus DNA ligase. Nucleic Acids Res. 24, 3079-3085.
14. Saiki, R.K., et al., & Erlich, H.A. (1998). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487-491.
15. Yang, S-W. & Chan, Y.H. (1992). Analysis of the formation of AMP-DNA intermediate and the successive reaction by human DNA ligase I and ligase II. J. Biol. Chem. 267, 8117-8122.
16. Matthews, B.W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
17. Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
18. Collaborative Computational Project, Number 4. (1994). The CCP4 suite: Programs for protein crystallography. Acta Cryst. D 50, 760-763.
19. Roussel, A. & Cambillau, C. (1989). TURBO-FRODO. In Silicon Graphics Geometry Partner Directory, pp 77-78, Silicon Graphics, Mountain View, CA.
20. Brünger, A.T., Karplus, M. & Petsko, G.A. (1989). Crystallographic refinement by simulated annealing: Application to crambin. Acta Cryst. A 45, 50-61.
21. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
22. Kraulis, P.J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-50.
23. Merritt, E.A. & Bacon, D.J. (1997). Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505-524.