The three-dimensional structure of the HRDC domain and implications for the werner and bloom syndrome proteins

Structure

Volumn 7, Issue 12, 1999, Pages 1557-1566

  Liu, Z ^a   Macias, M J ^a   Bottomley, M J ^a   Stier, G ^a   Linge, J P ^a   Nilges, M ^a   Bork, P ^a   Sattler, M ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Bloom syndrome; HRDC domain; NMR; RecQ helicases; Werner syndrome

Indexed keywords

HELICASE; RIBONUCLEASE; SINGLE STRANDED DNA BINDING PROTEIN;

ARTICLE; BLOOM SYNDROME; CARBOXY TERMINAL SEQUENCE; DNA BINDING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID METABOLISM; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; WERNER SYNDROME;

BACTERIA (MICROORGANISMS); SACCHAROMYCES CEREVISIAE;

EID: 0033573075     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)88346-X     Document Type: Article

References (65)

1. 1. Ellis, N.A. (1997). DMA helicases in inherited human disorders. Curr. Opin. Genet. Dev. 7, 354-363.
2. 2. Watt, P.M., Hickson, I.D., Borts, R.H. & Louis, E.J. (1996). SGS1, a homologue of the Bloom's and Werner's syndrome genes, is required for maintenance of genome stability in Saccharomyces cerevisiae. Genetics 144, 935-945.
3. 3. Sinclair, D.A., Mills, K. & Guarente, L. (1997). Accelerated aging and nucleolar fragmentation in yeast sgs1 mutants. Science 277, 1313-1316.
4. 4. Ellis, N.A., et al., & German, J. (1995). The Bloom's syndrome gene product is homologous to RecQ helicases. Cell 83, 655-666.
5. 5. Lu, J., Mullen, J.R., Brill, S.J., Kleff, S., Romeo, A.M. & Sternglanz, R. (1996). Human homologues of yeast helicase. Nature 383, 678-679.
6. 6. Yu, C.E., et al., & Schellenberg, G.D. (1996). Positional cloning of the Werner's syndrome gene. Science 272, 258-262.
7. 7. Morozov, V., Mushegian, A.R., Koonin, E.V. & Bork, P. (1997). A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases. Trends Biochem. Sci. 22, 417-418.
8. 8. Bahr, A., De Graeve, F., Kedinger, C. & Chatton, B. (1998). Point mutations causing Bloom's syndrome abolish ATPase and DNA helicase activities of the BLM protein. Oncogene 17, 2565-2571.
9. 9. Umezu, K., Nakayama, K. & Nakayama, H. (1990). Escherichia coli RecQ protein is a DNA helicase. Proc. Natl Acad. Sci. USA 87, 5363-5367.
10. 10. Umezu, K. & Nakayama, H. (1993). RecQ DNA helicase of Escherichia coli. Characterization of the helix-unwinding activity with emphasis on the effect of single-stranded DNA-binding protein. J. Mol. Biol. 230, 1145-1150.
11. 11. Gray, M.D., et al., & Loeb, L.A. (1997). The Werner syndrome protein is a DNA helicase. Nat. Genet. 17, 100-103.
12. 12. Karow, J.K., Chakraverty, R.K. & Hickson, I.D. (1997). The Bloom's syndrome gene product is a 3′-5′ DNA helicase. J. Biol. Chem. 272, 30611-30614.
13. 13. Bennett, R.J., Sharp, J.A. & Wang, J.C. (1998). Purification and characterization of the Sgs1 DNA helicase activity of Saccharomyces cerevisiae. J. Biol. Chem. 273, 9644-9650.
14. 14. Shen, J.C., Gray, M.D., Oshima, J. & Loeb, L.A. (1998). Characterization of Werner syndrome protein DNA helicase activity: directionality, substrate dependence and stimulation by replication protein A. Nucleic Acids Res. 26, 2879-2885.
15. 15. Watt, P.M., Louis, E.J., Borts, R.H. & Hickson, I.D. (1995), Sgs1: a eukaryotic homolog of E. coli RecQ that interacts with topoisomerase II in vivo and is required for faithful chromosome segregation. Cell 81, 253-260.
16. 16. Chakraverty, R.K. & Hickson, I.D. (1999). Defending genome integrity during DNA replication: a proposed role for RecQ family helicases. BioEssays 21, 286-294.
17. 17. Hanada, K., Ukita, T., Kohno, Y., Saito, K., Kato, J. & Ikeda, H. (1997). RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli. Proc. Natl Acad. Sci. USA 94, 3860-3865.
18. 18. Yamagata, K., Kato, J., Shimamoto, A., Goto, M., Furuichi, Y. & Ikeda, H. (1998). Bloom's and Werner's syndrome genes suppress hyperrecombination in yeast sgs1 mutant: implication for genomic instability in human diseases. Proc. Natl Acad. Sci. USA 95, 8733-8738.
19. 19. Yan, H., Chen, C.Y., Kobayashi, R. & Newport, J. (1998). Replication focus-forming activity 1 and the Werner syndrome gene product. Nat. Genet. 19, 375-378.
20. 20. Lebel, M. & Leder, P. (1998). A deletion within the murine Werner syndrome helicase induces sensitivity to inhibitors of topoisomerase and loss of cellular proliferative capacity. Proc. Natl Acad. Sci. USA 95, 13097-13102.
21. 21. Ge, Q., Frank, M.B., O'Brien, C. & Targoff, I.N. (1992). Cloning of a complementary DNA coding for the 100 kD antigenic protein of the PM-Scl autoantigen. J. Clin. Invest. 90, 559-570.
22. 22. Moser, M.J., Oshima, J. & Monnat, R.J., Jr (1999). WRN mutations in Werner syndrome. Hum. Mutat. 13, 271-279.
23. 23. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
24. 24. Korolev, S., Hsieh, J., Gauss, G.H., Lohman, T.M. & Waksman, G. (1997). Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90, 635-647.
25. 25. Subramanya, H.S., Bird, L.E., Brannigan, J.A. & Wigley, D.B. (1996). Crystal structure of a DExx box DNA helicase. Nature 384, 379-383.
26. 26. Velankar, S.S., Soultanas, P., Dillingham, M.S., Subramanya, H.S. & Wigley, D.B. (1999). Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75-84.
27. 27. Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J. & Pelletier, H. (1997). Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry 36, 11205-11215.
28. 28. Liu, D., Prasad, R., Wilson, S.H., DeRose, E.F. & Mullen, G.P. (1996). Three-dimensional solution structure of the N-terminal domain of DNA polymerase beta and mapping of the ssDNA interaction interface. Biochemistry 35, 6188-6200.
29. 29. Subramanya, H.S., Arciszewska, L.K., Baker, R.A., Bird, L.E., Sherratt, D.J. & Wigley, D.B. (1997). Crystal structure of the site-specific recombinase, XerD. EMBO J. 16, 5178-5187.
30. 30. Jeruzalmi, D. & Steitz, T.A. (1998). Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 17, 4101-4113.
31. 31. Sali, A. & Blundell, T.L. (1993). Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
32. 32. Gorbalenya, A.E. & Koonin, E.V. (1993). Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3, 419-429.
33. 33. Bird, L.E., Subramanya, H.S. & Wigley, D.B. (1998). Helicases: a unifying structural theme? Curr. Opin. Struct. Biol. 8, 14-18.
34. 34. Korolev, S., Yao, N., Lohman, T.M., Weber, P.C. & Waksman, G. (1998). Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 superfamilies of helicases. Protein Sci. 7, 605-610.
35. 35. Kusano, K., Berres, M.E. & Engels, W.R. (1999). Evolution of the RECQ family of helicases: a Drosophila homolog, Dmblm, is similar to the human Bloom syndrome gene. Genetics 151, 1027-1039.
36. 36. Fry, M. & Loeb, L.A. (1998). The three faces of the WS helicase. Nat. Genet. 19, 308-309.
37. 37. Matson, S.W., Bean, D.W. & George, J.W. (1994). DNA helicases: enzymes with essential roles in all aspects of DNA metabolism. BioEssays 16, 13-22.
38. 38. Dougherty, W.G., Carrington, J.C., Cary, S.M. & Parks, T.D. (1988). Biochemical and mutational analysis of a plant virus polyprotein cleavage site. EMBO J. 7, 1281-1287.
39. 39. Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Reifer, J. & Bax, A. (1995). NMRPipe: a multidimensional spectral processing system based on UNIX Pipes. J. Biomol. NMR 6, 277-293.
40. 40. Bartels, C., Xia, T.-H., Billeter, M., Güntert, P. & Wüthrich, K. (1995). The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR 5, 1-10.
41. 41. Clore, G.M. & Gronenborn, A.M. (1998). Determining the structures of large proteins and protein complexes by NMR. Tibtech 16, 22-34.
42. 42. Sattler, M., Schleucher, J. & Griesinger, C. (1999). Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. NMR Spectrosc. 34, 93-158.
43. 13C-labeled proteins via scalar couplings. J. Am. Chem. Soc. 115, 11054-11055.
44. 15N labeled proteins. J. Biomol. NMR 13, 5381-385.
45. 45. Fesik, S.W. & Zuiderweg, E.R.P. (1988). Heteronuclear three-dimensional NMR spectroscopy. A strategy for the simplification of homonuclear two-dimensional NMR spectra. J. Magn. Reson. 78, 588-593.
46. 46. Kuboniwa, H., Grzesiek, S., Delaglio, F. & Bax, A. (1994). Measurement of HN-Hα J-couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods. J. Biomol. NMR. 4, 871-878.
47. NCγ couplings in isotopically enriched proteins. J. Biomol. NMR 9, 323-328.
48. 48. Bodenhausen, G. & Ruben, D.J. (1980). Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem. Phys. Lett. 69, 185-189.
49. 13C labeling. Biochemistry 28, 7510-7516.
50. 50. Brünger, A.T., et al., & Warren, G.L. (1998). Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921.
51. 51. Nilges, M. & O'Donoghue, S.I. (1998). Ambiguous NOEs and automated NOESY assignment. Prog. NMR Spectrosc. 32, 107-139.
52. 52. Rice, L.M. & Brünger, A.T. (1994). Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19, 277-290.
53. 53. Stein, E.G., Rice, L.M. & Brünger, A.T. (1997). Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 124, 154-164.
54. 54. Folmer, R.H., Hilbers, C.W., Konings, R.N. & Nilges, M. (1997). Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data. J. Biomol. NMR 9, 245-258.
55. 1Hα dipolar and carbonyl chemical shift anisotropy relaxation interactions. J. Biomol. NMR 11, 213-220.
56. α chemical shifts and protein backbone conformation. J. Am. Chem. Soc. 119, 8070-8075.
57. 57. Linge, J.P. & Nilges, M. (1999). Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation. J. Biomol. NMR 13, 51-59.
58. 58. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R. & Thornton, J.M. (1996). AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR. 8, 477-486.
59. 59. Hooft, R.W., Vriend, G., Sander, C. & Abola, E.E. (1996). Errors in protein structures. Nature 381, 272.
60. 60. Koradi, R., Billeter, M. & Wüthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph, 14, 51-55.
61. 61. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 282.
62. 62. Piotto, M., Saudek, V. & Sklenar, V. (1992). Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2, 661-665.
63. 2O in protein NMR. Application to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc. 115, 12593-12594.
64. 64. Dailey, L., Yuan, H. & Basilico, C. (1994). Interaction between a novel F9-specific factor and octamer-binding proteins is required for cell-type-restricted activity of the fibroblast growth factor 4 enhancer. Mol. Cell. Biol. 14, 7758-7769.
65. 65. Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.