Structure and mechanism of helicases and nucleic acid translocases

Annual Review of Biochemistry

Volumn 76, Issue , 2007, Pages 23-50

  Singleton, Martin R ^a   Dillingham, Mark S ^b   Wigley, Dale B ^c  

^a London Research Institute   (United Kingdom)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

^c London Research Institute   (United Kingdom)

Author keywords

Atpase; Dna repair; Dna replication; Translocase

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; DEOXYCYTIDINE KINASE; DNA; DOUBLE STRANDED DNA; ENZYME; HELICASE; HELICASE DDA; HELICASE RECD; HELICASE UVRD; INITIATION FACTOR 4A; MINICHROMOSOME MAINTENANCE PROTEIN 2; MINICHROMOSOME MAINTENANCE PROTEIN 4; MINICHROMOSOME MAINTENANCE PROTEIN 5; MINICHROMOSOME MAINTENANCE PROTEIN 7; NONSTRUCTURAL PROTEIN 3; NUCLEIC ACID TRANSLOCASE; NUCLEOPROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RHO FACTOR; RNA HELICASE; SINGLE STRANDED DNA; SUPERFAMILY 1 HELICASE; SUPERFAMILY 1A HELICASE; SUPERFAMILY 1B HELICASE; SUPERFAMILY 2 HELICASE; SUPERFAMILY 3 HELICASE; SUPERFAMILY 4 HELICASE; SUPERFAMILY 5 HELICASE; SUPERFAMILY 6 HELICASE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; NUCLEIC ACID; PEPTIDYLTRANSFERASE;

AMINO ACID SEQUENCE; BACTERIOPHAGE; BACTERIUM; CATALYSIS; CELL FUNCTION; CHEMICAL ANALYSIS; CRYSTAL STRUCTURE; DNA REPLICATION; ENZYME ACTIVITY; GENE MUTATION; GENE TRANSLOCATION; GENETIC LINKAGE; GENETIC TRANSDUCTION; HEPATITIS C VIRUS; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; PROTEIN TARGETING; REGULATORY MECHANISM; REVIEW; RNA TRANSLATION; STOCHASTIC MODEL; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY; PROTEIN CONFORMATION; TRANSPORT AT THE CELLULAR LEVEL;

ADENOSINE TRIPHOSPHATE; ANIMALS; BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; DNA HELICASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACIDS; PEPTIDYL TRANSFERASES; PROTEIN CONFORMATION;

EID: 34548638261     PISSN: 00664154     EISSN: 00664154     Source Type: Book Series    
DOI: 10.1146/annurev.biochem.76.052305.115300     Document Type: Review

References (122)

1. Gorbalenya AE, Koonin EV. 1993. Curr. Biol. 3:419-29
2. Roman LJ, Kowalczykowski SC. 1989. Biochemistry 28:2873-81
3. Lohman TM, Bjornson KP. 1996. Annu. Rev. Biochem. 65:169-214
4. AliJA, Lohman TM. 1997. Science 275:377-80
5. Bianco PR, Kowalczykowski SC. 2000. Nature 405:368-72
6. Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco IJ, et al. 2006. Nature 439:105-8
7. rzbergerJP, BergerJM. 2006. Annu. Rev. Biophys. Biomol. Struct. 35:93-114
8. Pause A, Sonenberg N. 1992. EMBO J. 11:2643-54
9. Tanner NK, Cordin O, Banroques J, Doere M, Linder P. 2003. Mol. Cell 11:127-38
10. Korolev S, Yao N, Lohman TM, Weber PC, Waksman G. 1998. Protein Sci. 7:605-10
11. Mahdi AA, Briggs GS, Sharples GJ, Wen Q, Lloyd RG. 2003. EMBO J. 22:724-34
12. Ye J, Osborne AR, Groll M, Rapoport TA. 2004. Biochim. Biophys. Acta 1659:1-18
13. Walker JE, SarasteM, Runswick MJ, Gay NJ. 1982. EMBO J. 1:945-51
14. Scheffzek K, Ahmadian MR, Kabsch W, Wiesmuller L, Lautwein A, et al. 1997. Science 277:333-38
15. Nanduri B, Byrd AK, Eoff RL, Tackett AJ, Raney KD. 2002. Proc. Natl. Acad. Sci. USA 99:14722-27
16. Zhang XD, Dou SX, Xie P, HuJS, Wang PY, Xi XG. 2006. J. Biol. Chem. 281:12655-63
17. Dillingham MS, Webb MR, Kowalczykowski SC. 2005. J. Biol. Chem. 280:37069-77
18. Brendza KM, Cheng W, Fischer CJ, Chesnik MA, Niedziela-Majka A, Lohman TM. 2005. Proc. Natl. Acad. Sci. USA 102:10076-81
19. Bernstein DA, Zittel MC, Keck JL. 2003. EMBO J. 22:4910-21
20. Singleton MR, Wigley DB. 2002. J. Bacteriol. 184:1819-26
21. Subramanya HS, Bird LE, BranniganJA, Wigley DB. 1996. Nature 384:379-83
22. Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman G. 1997. Cell 90:635-47
23. Velankar SS, Soultanas P, DillinghamMS, Subramanya HS, Wigley DB. 1999. Cell97:75-84
24. Soultanas P, Dillingham MS, Velankar SS, Wigley DB. 1999. J. Mol. Biol. 290:137-48
25. Soultanas P, Dillingham MS, Wiley P, Webb MR, Wigley DB. 2000. EMBO J. 19:3799-810
26. DillinghamMS, Soultanas P, Wigley DB. 1999. Nucleic Acids Res. 27:3310-17
27. Dillingham MS, Wigley DB, Webb MR. 2000. Biochemistry 39:205-12
28. Dillingham MS, Soultanas P, Wiley P, Webb MR, Wigley DB. 2001. Proc. Natl. Acad. Sci. USA 98:8381-87
29. Soultanas P, Wigley DB. 2000. Curr. Opin. Struct. Biol. 10:124-28
30. Soultanas P, Wigley DB. 2001. Trends Biochem. Sci. 26:47-54
31. Yarranton GT, Gefter ML. 1979. Proc. Natl. Acad. Sci. USA 76:1658-62
32. Ivessa AS, Zhou JQ, Schulz VP, Monson EK, ZakianVA. 2002. Genes Dev. 16:1383-96
33. Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB. 2004. Nature 432:187-93
34. Taylor AF, Smith GR. 1995. J. Biol. Chem. 270:24451-58
35. Ha T, Rasnik I, Cheng W, Babcock HP, Gauss GH, et al. 2002. Nature 419:638-41
36. Fischer CJ, Maluf NK Lohman TM. 2004. J. Mol. Biol. 344:1287-309
37. AliJA, Maluf NK, Lohman TM. 1999. J. Mol. Biol. 293:815-34
38. Byrd AK, Raney KD. 2004. Nat. Struct. Mol. Biol. 11:531-38
39. Byrd AK, Raney KD. 2005. Biochemistry 44:12990-97
40. Cordin O, Banroques J, Tanner NK, Linder P. 2006. Gene 367:17-37
41. Bennett RJ, Keck JL. 2004. Crit. Rev. Biochem. Mol. Biol. 39:79-97
42. Flaus A, Owen-Hughes T. 2004. Curr. Opin. Genet. Dev. 14:165-73
43. Flaus A, Martin DM, Barton GJ, Owen-Hughes T. 2006. Nucleic Acids Res. 34:2887-905
44. Linder P, Lasko P. 2006. Cell 125:219-21
45. Pang PS,Jankowsky E, Planet PJ, Pyle AM. 2002. EMBO J. 21:1168-76
46. Tai CL, Chi WK, Chen DS, Hwang LH. 1996. J. Virol. 70:8477-84
47. Levin MK, Wang YH, Patel SS. 2004. J. Biol. Chem. 279:26005-12
48. Tackett AJ, Chen Y, Cameron CE, Raney KD. 2005. J. Biol. Chem. 280:10797-806
49. Kim JL, Morgenstern KA, Griffith JP, Dwyer MD, Thomson JA, et al. 1998. Structure 6:89-100
50. Mackintosh SG, Lu JZ, Jordan JB, Harrison MK, Sikora B, et al. 2006. J. Biol. Chem. 281:3528-35
51. Kim JW, Seo MY, Shelat A, Kim CS, Kwon TW, et al. 2003. J. Virol. 77:571-82
52. Tai CL, Pan WC, Liaw SH, Yang UC, Hwang LH, Chen DS. 2001. J. Virol. 75:8289-97
53. Paolini C, Lahm A, De Francesco R, Gallinari P. 2000. J. Gen. Virol. 81:1649-58
54. Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. 2006. Cell 125:287-300
55. Serebrov V, Pyle AM. 2004. Nature 430:476-80
56. Jankowsky E, Gross CH, Shuman S, Pyle AM. 2000. Nature 403:447-51
57. Kawaoka J, Jankowsky E, Pyle AM. 2004. Nat. Struct. Mol. Biol. 11:526-30
58. BeranRK, Bruno MM, Bowers HA, Jankowsky E, Pyle AM. 2006. J.Mol. Biol. 358:974-82
59. Levin MK, GurjarMM, Patel SS. 2003. J. Biol. Chem. 278:23311-16
60. Levin MK, GurjarM, Patel SS. 2005. Nat. Struct. Mol. Biol. 12:429-35
61. Fairman ME, Maroney PA, Wang W, Bowers HA, Gollnick P, et al. 2004. Science 304:730-34
62. Stanley LK, Seidel R, van der Scheer C, Dekker NH, Szczelkun MD, Dekker C. 2006. EMBO J. 25:2230-39
63. Firman K, Szczelkun MD. 2000. EMBO J. 19:2094-102
64. Levy O, Ptacin JL, Pease PJ, Gore J, Eisen MB, et al. 2005. Proc. Natl. Acad. Sci. USA 102:17618-23
65. Whitehouse I, Stockdale C, Flaus A, Szczelkun MD, Owen-Hughes T. 2003. Mol. Cell. Biol. 23:1935-45
66. Jaskelioff M, Van Komen S, Krebs JE, Sung P, Peterson CL. 2003. J. Biol. Chem. 278:9212-18
67. Durr H, Korner C, Muller M, Hickmann V, Hopfner KP. 2005. Cell 121:363-73
68. Caruthers. JM, Johnson ER, McKay DB. 2000. Proc. Natl. Acad. Sci. USA 97:13080-85
69. Thoma NH, Czyzewski BK, Alexeev AA, Mazin AV, Kowalczykowski SC, Pavletich NP. 2005. Nat. Struct. Mol. Biol. 12:350-56
70. Hunt JF, Weinkauf S, Henry L, FakJJ, McNicholas P, et al. 2002. Science 297:2018-26
71. Tomkiewicz D, Nouwen N, van Leeuwen R, Tans S, Driessen AJM. 2006. J. Biol. Chem. 281:15709-13
72. Park SK, Kim DW, Choe J, Kim H. 1997. Biochem. Biophys. Res. Commun. 235:593-97
73. Rudolf J, Makrantoni V, Ingledew WJ, Stark MJR, White MF. 2006. Mol. Cell 23:801-8
74. Singleton MR, Scaife S, Wigley DB. 2001. Cell 107:79-89
75. Diges CM, Uhlenbeck OC. 2001. EMBO J. 20:5503-12
76. Grune T, BrzeskiJ, Eberharter A, Clapier CR, Corona DF, et al. 2003. Mol. Cell 12:449-60
77. Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, t al. 2006. Cell 124:507-20
78. Jankowsky E, Gross CH, Shuman S, Pyle AM. 2001. Science 291:121-25
79. Linder P, Tanner NK, Banroques J. 2001. TrendsBiochem. Sci. 26:339-41
80. Davey MJ, O'DonnellM. 2003. Curr. Biol. 13:R594-96
81. Gorbalenya AE, Koonin EV, Wolf YI. 1990. FEBS Lett. 262:145-48
82. Hickman AB, Dyda F. 2005. Curr. Opin. Struct. Biol. 15:77-85
83. Enemark EJ, Joshua-Tor L. 2006. Nature 442:270-75
84. Singleton MR, Sawaya MR, Ellenberger T, Wigley DB. 2000. Cell 101:589-600
85. Ilyina TV, Gorbalenya AE, Koonin EV. 1992. J. Mol. Evol. 34:351-57
86. TothEA, Li Y, Sawaya MR, Cheng Y, Ellenberger T. 2003. Mol. Cell 12:1113-23
87. Sawaya MR, Guo S, Tabor S, Richardson CC, Ellenberger T. 1999. Cell 99:167-77
88. Washington MT, Rosenberg AH, Griffin K, Studier FW, Patel SS. 1996. J. Biol. Chem. 271:26825-34
89. NiedenzuT, Roleke D, Bains G, Scherzinger E, Saenger W. 2001. J. Mol. Biol. 306:479-87
90. Yu X, Jezewska MJ, Bujalowski W, Egelman EH. 1996. J. Mol. Biol. 259:7-14
91. Barcena M, Martin CS, Weise F, Ayora S, Alonso JC, Carazo JM. 1998. J. Mol. Biol. 283:809-19
92. Barcena M, Ruiz T, Donate LE, Brown SE, Dixon NE, et al. 2001. EMBO J. 20:1462-68
93. Gogol EP, Seifried SE, von Hippel PH. 1991. J. Mol. Biol. 221:1127-38
94. Skordalakes E, Berger JM. 2003. Cell 114:135-46
95. Labib K, Tercero JA, DiffleyJF. 2000. Science 288:1643-47
96. Kaplan DL, O'Donnell M. 2004. Mol. Cell 15:453-65
97. Chong JP, Hayashi MK, Simon MN, Xu RM, Stillman B. 2000. Proc. Natl. Acad. Sci. USA 97:1530-35
98. Pape T, Meka H, Chen S, Vicentini G, van Heel M, Onesti S. 2003. EMBO Rep. 4:1079-83
99. Fletcher RJ, Bishop BE, Leon RP, Sclafani RA, Ogata CM, Chen XS. 2003. Nat. Struct. Biol. 10:160-67
100. West SC. 1996. J. Bacteriol. 178:1237-41
101. Putnam CD, Clancy SB, Tsuruta H, Gonzalez S, Wetmur JG, Tainer JA. 2001. J. Mol. Biol. 311:297-310
102. Yamada K, Kunishima N, Mayanagi K, Ohnishi T, Nishino T, et al. 2001. Proc. Natl. Acad. Sci. USA 98:1442-47
103. Bigot S, Saleh OA, Lesterlin C, Pages C, El KarouiM, et al. 2005. EMBO J. 24:3770-80
104. Massey TH, Mercogliano CP, Yates J, Sherratt DJ, Lowe J. 2006. Mol. Cell 23:457-69
105. Gomis-Ruth FX, Moncalian G, Perez-Luque R, Gonzalez A, Cabezon E, et al. 2001. Nature 409:637-41
106. Mancini EJ, Kainov DE, Grimes. JM, Tuma R, Bamford DH, Stuart DI. 2004. Cell 118:743-55
107. Bujalowski W, Klonowska MM. 1993. Biochemistry 32:5888-900
108. Hingorani MM, Washington MT, Moore KC, Patel SS. 1997. Proc. Natl. Acad. Sci. USA 94:5012-17
109. Abrahams JP, Leslie AG, Lutter R, Walker JE. 1994. Nature 370:621-28
110. Hingorani MM, Patel SS. 1996. Biochemistry 35:2218-28
111. Stitt BL, XuY. 1998. J. Biol. Chem. 273:26477-86
112. LiaoJC, Jeong YJ, Kim DE, Patel SS, Oster G. 2005. J. Mol. Biol. 350:452-75
113. AdelmanJL, Jeong YJ, LiaoJC, Patel G, Kim DE, et al. 2006. Mol. Cell 22:611-21
114. Crampton DJ, Mukherjee S, Richardson CC. 2006. Mol. Cell 21:165-74
115. Martin A, Baker TA, Sauer RT. 2005. Nature 437:1115-20
116. Gai DH, Zhao R, Li DW, Finkielstein CV, Chen XS. 2004. Cell 119:47-60
117. Huang SG, Weisshart K, Fanning E. 1998. Biochemistry 37:15336-44
118. Galletto R, Jezewska MJ, Bujalowski W. 2004. J. Mol. Biol. 343:83-99
119. Kim DE, NarayanM, Patel SS. 2002. J. Mol. Biol. 321:807-19
120. Kaplan DL. 2000. J. Mol. Biol. 301:285-99
121. YuX, Hingorani MM, Patel SS, Egelman EH. 1996. Nat. Struct. Biol. 3:740-43
122. Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, et al. 1996. Science 274:415-21