Nucleic acid recognition by OB-fold proteins

Annual Review of Biophysics and Biomolecular Structure

Volumn 32, Issue , 2003, Pages 115-133

  Theobald, Douglas L ^a   Mitton Fry, Rachel M ^a   Wuttke, Deborah S ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Protein fold; Single stranded; Structural alignment

Indexed keywords

BACTERIAL PROTEIN; FUNGAL PROTEIN; NUCLEIC ACID; OB FOLD PROTEIN; PROTEIN; PROTEIN L2; PROTEIN S II; PROTEIN S17; RIBOSOME PROTEIN; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

COMPLEX FORMATION; ESCHERICHIA COLI; HALOARCULA MARISMORTUI; HUMAN; LIGAND BINDING; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; REVIEW; SACCHAROMYCES CEREVISIAE;

AMINO ACID MOTIFS; DNA; DNA-BINDING PROTEINS; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; OLIGONUCLEOTIDES; OLIGOSACCHARIDES; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RNA;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; HALOARCULA; HALOARCULA MARISMORTUI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0012767432     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.32.110601.142506     Document Type: Review

References (80)

1. Allison TJ, Wood TC, Briercheck DM, Rastinejad F, Richardson JP, Rule GS. 1998. Crystal structure of the RNA-binding domain from transcription termination factor rho. Nat. Struct. Biol. 5:352-56
2. Anderson EM, Halsey WH, Wuttke DS. 2002. Delineation of the high-affinity single-stranded telomeric DNA-binding domain of S. cerevisiae Cdc13. Nucleic Acids Res. 30:4305-13
3. Anderson EM, Halsey WH, Wuttke DS. 2002. Site-directed mutagenesis reveals the thermodynamic requirements for single-stranded DNA recognition by the telomere-binding protein Cdc13. Biochemistry 42:In press
4. Antson AA. 2000. Single stranded RNA binding proteins. Curr. Opin. Struct. Biol. 10:87-94
5. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289:905-20
6. Bastin-Shanower SA, Brill SJ. 2001. Functional analysis of the four DNA binding domains of replication protein A. The role of RPA2 in ssDNA binding. J. Biol. Chem. 276:36446-53
7. Battiste JL, Pestova TV, Hellen CUT, Wagner G. 2000. The eIF1A solution structure reveals a large RNA-binding surface important for scanning function. Mol. Cell 5:109-19
8. Berthet-Colominas C, Seignovert L, Härtlein M, Grotli M, Cusack S, Leberman R. 1998. The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. EMBO J. 17:2947-60
9. Bochkareva E, Belegu V, Korolev S, Bochkarev A. 2001. Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J. 20:612-18
10. Bochkarev A, Bochkareva E, Frappier L, Edwards AM. 1999. The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding. EMBO J. 18:4498-504
11. Bochkareva E, Korolev S, Lees-Miller SP, Bochkarev A. 2002. Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA. EMBO J. 21:1855-63
12. Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L. 1997. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385:176-81
13. Bogden CE, Fass D, Bergman N, Nichols MD, Berger JM. 1999. The structural basis for terminator recognition by the rho transcription termination factor. Mol. Cell 3:487-93
14. Brennan CA, Dombroski AJ, Platt T. 1987. Transcription termination factor rho is an RNA-DNA helicase. Cell 48:945-52
15. Briercheck DM, Wood TC, Allison TJ, Richardson JP, Rule GS. 1998. The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions. Nat. Struct. Biol. 5:393-99
16. Brodersen DE, Clemons WM Jr, Carter AP, Wimbedy BT, Ramakrishnan V. 2002. Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA. J. Mol. Biol. 316:725-68
17. Bycroft M, Hubbard TJP, Proctor M, Freund SMV, Murzin AG. 1997. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell 88:235-42
18. Carter AP, Clemons WM Jr, Brodersen DE, Morgan-Warren RJ, Hartsch T, et al. 2001. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291:498-501
19. Asp recognition by its cognate class II aminoacyl-tRNA synthetase. Nature 362:181-84
20. Chédin F, Seitz EM, Kowalczykowski SC. 1998. Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins. Trends Biochem. Sci. 23:273-77
21. Classen S, Ruggles JA, Schultz SC. 2001. Crystal structure of the N-terminal domain of Oxytricha nova telomere end-binding protein α subunit both uncomplexed and complexed with telomeric ssDNA. J. Mol. Biol. 314:1113-25
22. Lys. J. Mol. Biol. 253:100-13
23. Diedrich G, Spahn CMT, Stelzl U, Schäfer MA, Wooten T, et al. 2000. Ribosomal protein L2 is involved in the association of the ribosomal subunits, tRNA binding to A and P sites and peptidyl transfer. EMBO J. 19:5241-50
24. Dolan JW, Marshall NF, Richardson JP. 1990. Transcription termination factor rho has three distinct structural domains. J. Biol. Chem. 265:5747-54
25. Dombroski AJ, Platt T. 1988. Structure of rho factor: an RNA-binding domain and a separate region with strong similarity to proven ATP-binding domains. Proc. Natl. Acad. Sci. USA 85:2538-42
26. Egebjerg J, Christiansen J, Garrett RA. 1991. Attachment sites of primary binding proteins L1, L2 and L23 on 23S ribosomal RNA of Escherichia coli. J. Mol. Biol. 222:251-64
27. Asp in Escherichia coli - a snapshot of the second step. EMBO J. 18:6532-41
28. Evans SK, Lundblad V. 1999. Est1 and Cdc13 as comediators of telomerase access. Science 286:117-20
29. Froelich-Ammon SJ, Dickinson BA, Bevilacqua JM, Schultz SC, Cech TR. 1998. Modulation of telomerase activity by telomere DNA-binding proteins in Oxytricha. Genes Dev. 12:1504-14
30. Garvik B, Carson M, Hartwell L. 1995. Single-stranded DNA arising at telomeres in cdc13 mutants may constitute a specific signal for the RAD9 checkpoint. Mol. Cell Biol. 15:6128-38
31. 15N NMR. Biochemistry 32:12812-20
32. Phe. Structure 5:59-68
33. Gottschling DE, Zakian VA. 1986. Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA. Cell 47:195-205
34. Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, et al. 2001. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107:679-88
35. Horvath MP, Schultz SC. 2001. DNA G-quartets in a 1.86 Å resolution structure of an Oxytricha nova telomeric protein-DNA complex. J. Mol. Biol. 310:367-77
36. Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA, Schultz SC. 1998. Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA. Cell 95:963-74
37. Hubbard SJ, Thornton JM. 1993. NACCESS, computer program. London: Dep. Biochem. Mol. Biol., University College
38. Hughes TR, Weilbaecher RG, Walterscheid M, Lundblad V. 2000. Identification of the single-strand telomeric DNA binding domain of the Saccharomyces cerevisiae Cdc13 protein. Proc. Natl. Acad. Sci. USA 97:6457-62
39. Iftode C, Daniely Y, Borowiec JA. 1999. Replication protein A (RPA): the eukaryotic SSB. Crit. Rev. Biochem. Mol. Biol. 34:141-80
40. Jacobs DM, Lipton AS, Isern NG, Daughdrill GW, Lowry DF, et al. 1999. Human replication protein A: Global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker. J. Biol. NMR 14:321-31
41. Jaishree TN, Ramakrishnan V, White SW. 1996. Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy. Biochemistry 35:2845-53
42. Kelly TJ, Simancek P, Brush GS. 1998. Identification and characterization of a single-stranded DNA-binding protein from the archaeon Methanococcus jannaschii. Proc. Natl. Acad. Sci. USA 95:14634-39
43. Khaitovich P, Mankin AS, Green R, Lancaster L, Noller HF. 1999. Characterization of functionally active subribosomal particles from Thermus aquaticus. Proc. Natl. Acad. Sci. USA 96:85-90
44. Kim C, Snyder RO, Wold MS. 1992. Binding properties of replication protein A from human and yeast cells. Mol. Cell Biol. 12:3050-59
45. Kleywegt GJ. 1996. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D 52:842-57
46. α coordinates alone. J. Mol. Biol. 273:371-75
47. Koradi R, Billeter M, Wüthrich K. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:51-55
48. Kraulis PJ. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-50
49. Li W, Hoffman DW. 2001. Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy. Protein Sci. 10:2426-38
50. 1-3 telomeric DNA-binding protein in vitro that affects telomere behavior in vivo. Proc. Natl. Acad. Sci. USA 93:13760-65
51. Lohman TM, Ferrari ME. 1994. Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu. Rev. Biochem. 63:527-70
52. McGlynn P, Lloyd RG. 2000. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell 101:35-45
53. McGlynn P, Lloyd RG. 2001. Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation. Proc. Natl. Acad. Sci. USA 98:8227-34
54. McGlynn P, Mahdi AA, Lloyd RG. 2000. Characterisation of the catalytically active form of RecG helicase. Nucleic Acids Res. 28:2324-32
55. Merritt EA, Bacon DJ. 1997. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:505-24
56. Mitton-Fry RM, Anderson EM, Hughes TR, Lundblad V, Wuttke DS. 2002. Conserved structure for single-stranded telomeric DNA recognition. Science 296:145-47
57. Murzin AG. 1993. OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for nonhomologous sequences. EMBO J. 12:861-67
58. Murzin AG. 1998. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8:380-87
59. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-40
60. Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M, Tanaka I. 1999. The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome. EMBO J. 18:1459-67
61. Nugent CI, Hughes TR, Lue NF, Lundblad V. 1996. Cdc13p: a single-strand telomeric DNA-binding protein with a dual role in yeast telomere maintenance. Science 274:249-52
62. Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakristman V. 2001. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292:897-902
63. Peersen OB, Ruggles JA, Schultz SC. 2002. Dimeric structure of the Oxytricha nova telomere end-binding protein α-subunit bound to ssDNA. Nat. Struct. Biol. 9:182-87
64. Pennock E, Buckley K, Lundblad V. 2001. Cdc13 delivers separate complexes to the telomere for end protection and replication. Cell 104:387-96
65. Price CM, Cech TR. 1987. Telomeric DNA-protein interactions of Oxytricha macronuclear DNA. Genes Dev. 1:783-93
66. Aso by cognate aspartyl-tRNA synthetase. Science 252:1696-99
67. Raghunathan S, Kozlov AG, Lohman TM, Waksman G. 2000. Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol. 7:648-52
68. Raghunathan S, Ricard CS, Lohman TM, Waksman G. 1997. Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-Å resolution. Proc. Natl. Acad. Sci. USA 94:6652-57
69. Asp. Science 252:1682-89
70. Russell RB, Barton GJ. 1992. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 14:309-23
71. Sette M, van Tilborg P, Spurio R, Kaptein R, Paci M, et al. 1997. The structure of the translational initiation factor IF1 from E. coli contains an oligomer-binding motif. EMBO J. 16:1436-43
72. Shamoo Y, Friedman AM, Parsons MR, Konigsberg WH, Steitz TA. 1995. Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Nature 376:362-66
73. Singleton MR, Scaife S, Wigley DB. 2001. Structural analysis of DNA replication fork reversal by RecG. Cell 107:79-89
74. Suck D. 1997. Common fold, common function, common origin? Nat. Struct. Biol. 4:161-65
75. Swofford DL. 2002. PAUP* 4.0 - Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, MA: Sinauer Assoc.
76. Wang Y, von Hippel PH. 1993. Escherichia coli transcription termination factor rho. II. Binding of oligonucleotide cofactors. J. Biol. Chem. 268:13947-55
77. Webster G, Genschel J, Curth U, Urbanke C, Kang C, Hilgenfeld R. 1997. A common core for binding single-stranded DNA: structural comparison of the single-stranded DNA-binding proteins (SSB) from E. coli and human mitochondria. FEBS Lett. 411:313-16
78. Williamson JR. 2000. Induced fit in RNA-protein recognition. Nat. Struct. Biol. 7:834-37
79. Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, et al. 2000. Structure of the 30S ribosomal subunit. Nature 407:327-39
80. Wold MS. 1997. Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66:61-92