Prokaryotic DNA‐binding Proteins

DNA-binding proteins are found in all organisms and play critical roles in DNA metabolism. Structure–function studies can be carried out on single-strand specific binding proteins (SSBs), which function in DNA replication, recombination and repair.

Keywords: DNA-binding protein; single-strand specific binding protein; protein domains; protein–protein interaction; cooperativity

Figure 1. Domain structure of gene 32 protein. *I is the truncated product created by the loss of the N-terminal (‘B’) domain; *II is the truncated product created by the C-terminal (‘A’) domain; *III, the core domain, is created by loss of both terminal domains.
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 References
    Bogdarina I, Fox DG and Kneale GG (1998) Equilibrium and kinetic binding analysis of the N-terminal domain of the Pf1 gene 5 protein and its interaction with single-stranded DNA. Journal of Molecular Biology 275: 443–452.
    Casas-Finet JR, Fischer KR and Karpel RL (1992) Structural basis for the nucleic acid binding cooperativity of bacteriophage T4 gene 32 protein: the (Lys/Arg)3(Ser/Thr)2 (LAST) motif. Proceedings of the National Academy of Sciences of the USA 89: 1050–1054.
    Cho NY, Choi M and Rothman-Denes LB (1995) The bacteriophage N4-coded single-stranded DNA-binding protein (N4SSB) is the transcriptional activator of Escherichia coli RNA polymerase at N4 late promoters. Journal of Molecular Biology 246: 461–471.
    Choi M, Miller A, Cho NY and Rothman-Denes LB (1995) Identification, cloning, and characterization of the bacteriophage N4 gene encoding the single-stranded DNA-binding protein. A protein required for phage replication, recombination, and late transcription. Journal of Biological Chemistry 270: 22541–22547.
    Gascon I, Gutierrez C and Salas M (2000) Structural and functional comparative study of the complexes formed by viral 29, Nf and GA-1 SSB proteins with DNA. Journal of Molecular Biology 296: 989–999.
    Gray CW (1989) Three-dimensional structure of complexes of single-stranded DNA-binding proteins with DNA. IKe and fd gene 5 proteins form left-handed helices with single-stranded DNA. Journal of Molecular Biology 208: 57–64.
    Hurley JM, Chervitz SA, Jarvis TC, Singer BS and Gold L (1993) Assembly of the bacteriophage T4 replication machine requires the acidic carboxy terminus of gene 32 protein. Journal of Molecular Biology 229: 398–418.
    book Karpel RL (1990) "T4 Bacteriophage gene 32 protein". In: Revzin A (ed.) The Biology of Non-Specific DNA–Protein Interactions, pp. 103–130. Boca Raton, FL: CRC Press
    Kelly TJ, Simancek P and Brush GS (1998) Identification and characterization of a single-stranded DNA-binding protein from the archaeon Methanococcus jannaschii. Proceedings of the National Academy of Sciences of the USA 95: 14634–14639.
    Kong D and Richardson CC (1998) Role of the acidic carboxyl-terminal domain of the single-stranded DNA-binding protein of bacteriophage T7 in specific protein–protein interactions. Journal of Biological Chemistry 273: 6556–6564.
    book Kornberg A and Baker TA (1992) DNA Replication, 2nd edn., pp. 345–347. New York: WH Freeman.
    Kowalczykowski SC, Lonberg N, Newport JW and von Hippel PH (1981) Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. I. Characterization of the binding interactions. Journal of Molecular Biology 145: 75–104.
    Kowalczykowski SC, Paul LS, Lonberg N et al. (1986) Cooperative and noncooperative binding of protein ligands to nucleic acid lattices: experimental approaches to the determination of thermodynamic parameters. Biochemistry 25: 1226–1240.
    proceedings Krassa KB, Green LS and Gold L (1991) Protein–protein interactions with the acidic COOH terminus of the single-stranded DNA-binding protein of the bacteriophage T4. Proceedings of the National Academy of Sciences of the USA 88: 4010–4014.
    Lohman TM and Bujalowski W (1991) Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein–DNA interactions: spectroscopic approaches to monitor binding. Methods Enzymology 208: 258–290.
    Lohman TM and Ferrari ME (1994) Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annual Review of Biochemistry 63: 527–570.
    Lonberg N, Kowalczykowski SC, Paul LS and von Hippel PH (1981) Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. III. Binding properties of two specific proteolytic digestion products of the protein (G32P*I and G32P*III). Journal of Molecular Biology 145: 123–138.
    McGhee JD and Hippel PH v (1974) Theoretical aspects of DNA–protein interactions: co-operative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice. Journal of Molecular Biology 86: 469–489.
    McPheeters DS, Stormo GD and Gold L (1988) Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA. Journal of Molecular Biology 201: 517–535.
    book Nossal NG (1994) "The bacteriophage T4 replication fork". In: Karam JD (ed.) Molecular Biology of Bacteriophage T4, pp. 43–53. Washington, DC: American Society for Microbiology
    Raghunathan S, Kozlov AG, Lohman TM and Waksman G (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Native Structural Biology 7: 648–652.
    Record MT Jr, Lohman ML and De Haseth P (1976) Ion effects on ligand–nucleic acid interactions. Journal of Molecular Biology 107: 145–158.
    book Revzin A (1990) "Techniques for characterizing nonspecific DNA–protein interactions". In: Revzin A (ed.) The Biology of Nonspecific DNA–Protein Interactions, pp. 5–31. Boca Raton, FL: CRC Press
    Schwarz K, Hansen-Hagge T and Bartram C (1990) Improved yields of long PCR products using gene 32 protein. Nucleic Acids Research 18: 1079.
    Shamoo Y, Friedman AM, Parsons MR, Konigsberg WH and Steitz TA (1995) Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Nature 376: 362–366.
    proceedings Skinner MM, Zhang H, Leschnitzer DH et al. (1994) Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein. Proceedings of the National Academy of Sciences of the USA 91: 2071–2075.
    Villemain JL and Giedroc DP (1993) Energetics of arginine-4 substitution mutants in the N-terminal cooperativity domain of T4 gene 32 protein. Biochemistry 32: 11235–11246.
    von Hippel PH, Kowalczykowski SC, Lonberg N et al. (1982) Autoregulation of gene expression. Quantitative evaluation of the expression and function of the bacteriophage T4 gene 32 (single-stranded DNA binding) protein system. Journal of Molecular Biology 162: 795–818.
    Waidner LA, Flynn EK, Wu M, Li X and Karpel RL (2001) Domain effects on the DNA-interactive properties of bacteriophage T4 gene 32 protein. Journal of Biological Chemistry 276: 2509–2516.
    Wheeler LJ, Ray NB, Ungermann C et al. (1996) T4 phage gene 32 protein as a candidate organizing factor for the deoxyribonucleoside triphosphate synthetase complex. Journal of Biological Chemistry 271: 11156–11162.
    book Young MC, Reddy MK, Jarvis TC et al. (1994) "Protein–protein and protein–DNA interactions in the T4 DNA polymerase accessory protein complex". In: Karam JD (ed.) Molecular Biology of Bacteriophage T4, pp. 313–317. Washington, DC: American Society for Microbiology
    Zaman G, Smetsers A, Kaan A, Schoenmakers J and Konings R (1991) Regulation of expression of the genome of bacteriophage M13. Gene V protein regulated translation of the mRNAs encoded by genes I, III, V and X. Biochimica Biophysica Acta 1089: 183–192.
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Karpel, Richard L(Apr 2001) Prokaryotic DNA‐binding Proteins. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0001042]