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Gene Review

T7p29  -  DNA polymerase

Enterobacteria phage T7

 
 
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Disease relevance of T7p29

 

High impact information on T7p29

  • First, the clone-encoded protein is immunologically related to DNA polymerase I. Second, cells containing the gene cloned in the high copy number plasmid YEp24 overproduce the polymerase activity 4- to 5-fold as measured in yeast extracts [6].
  • The DNA polymerase from phage phi29 is a B family polymerase that initiates replication using a protein as a primer, attaching the first nucleotide of the phage genome to the hydroxyl of a specific serine of the priming protein [7].
  • The replisome consisting of bacteriophage T7 DNA polymerase, helicase, primase, and single-stranded DNA-binding protein mediates coordinated replication [8].
  • Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase [9].
  • Mutations of the corresponding tyrosine in DNA polymerase (DNAP) I increase miscoding, though effects on dNTP/rNTP discrimination for the DNAP I mutations have not been reported [10].
 

Chemical compound and disease context of T7p29

 

Biological context of T7p29

 

Anatomical context of T7p29

 

Associations of T7p29 with chemical compounds

  • The lack of discrimination against dideoxynucleoside triphosphates using T7 DNA polymerase and Mn2+ results in uniform terminations of DNA sequencing reactions, with the intensity of adjacent bands on polyacrylamide gels varying in most instances by less than 10% [11].
  • The exchange can be monitored by the use of a genetically altered T7 DNA polymerase (gp5-Y526F) in which tyrosine-526 is replaced with phenylalanine [22].
  • After a final phosphocellulose chromatography, T7 DNA polymerase of better than 99% purity, as estimated from sodium dodecyl sulfate polyacrylamide gel electrophoresis, is obtained [21].
  • Results with a mutant T7 DNA polymerase in which aliphatic residues are substituted for these amino acids and experiments with different length and methylphosphonate-modified primer-templates demonstrate that these interactions are essential for processive synthesis and d(A.T)(n) tract bypass [23].
  • Beta-L-thymidine 5'-triphosphate analogs as DNA polymerase substrates [14].
 

Physical interactions of T7p29

 

Regulatory relationships of T7p29

  • The T7 gene 4 protein acts processively as helicase to promote leading strand synthesis and distributively as primase to initiate lagging strand synthesis by T7 DNA polymerase [25].
 

Other interactions of T7p29

 

Analytical, diagnostic and therapeutic context of T7p29

  • Analysis by electron microscopy shows that T7 DNA polymerase [DNA nucleotidyltransferase (DNA-directed), EC 2.7.7.7] and gene 4 protein initiate DNA synthesis at randomly located nicks on duplex DNA to produce branched molecules [30].
  • GP2.5-delta 21C does not physically interact with T7 DNA polymerase as measured by affinity chromatography and fluorescent emission anisotropy [31].
  • Measurements of surface plasmon resonance indicate that a monomer of T7 DNA polymerase binds to a dimer of gp4, gp4-C219, or gp4-C241 but to a monomer of gp4-C272 [32].
  • T7 DNA polymerase and gene 4 protein associate to form a complex that can be isolated by filtration through a molecular sieve [33].
  • T7 DNA polymerase forms a stable complex with single-stranded M13 DNA at 50 mM NaCl as measured by gel filtration, and this complex requires 200 mM NaCl for dissociation, a salt concentration that inhibits RNA-primed DNA synthesis [33].

References

  1. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Doublié, S., Tabor, S., Long, A.M., Richardson, C.C., Ellenberger, T. Nature (1998) [Pubmed]
  2. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Sawaya, M.R., Pelletier, H., Kumar, A., Wilson, S.H., Kraut, J. Science (1994) [Pubmed]
  3. The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I. Bedford, E., Tabor, S., Richardson, C.C. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  4. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. Tabor, S., Richardson, C.C. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  5. Real-time kinetics of the interaction between the two subunits, Escherichia coli thioredoxin and gene 5 protein of phage T7 DNA polymerase. Singha, N.C., Vlamis-Gardikas, A., Holmgren, A. J. Biol. Chem. (2003) [Pubmed]
  6. Isolation of the gene encoding yeast DNA polymerase I. Johnson, L.M., Snyder, M., Chang, L.M., Davis, R.W., Campbell, J.L. Cell (1985) [Pubmed]
  7. Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Kamtekar, S., Berman, A.J., Wang, J., Lázaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A. Mol. Cell (2004) [Pubmed]
  8. Coordinated leading and lagging strand DNA synthesis on a minicircular template. Lee, J., Chastain, P.D., Kusakabe, T., Griffith, J.D., Richardson, C.C. Mol. Cell (1998) [Pubmed]
  9. Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. Brieba, L.G., Eichman, B.F., Kokoska, R.J., Doublié, S., Kunkel, T.A., Ellenberger, T. EMBO J. (2004) [Pubmed]
  10. A mutant T7 RNA polymerase as a DNA polymerase. Sousa, R., Padilla, R. EMBO J. (1995) [Pubmed]
  11. Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. Tabor, S., Richardson, C.C. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  12. Kinetics of nucleotide incorporation opposite DNA bulky guanine N2 adducts by processive bacteriophage T7 DNA polymerase (exonuclease-) and HIV-1 reverse transcriptase. Zang, H., Harris, T.M., Guengerich, F.P. J. Biol. Chem. (2005) [Pubmed]
  13. Bacteriophage T7 deoxyribonucleic acid replication invitro. Bacteriophage T7 DNA polymerase: an an emzyme composed of phage- and host-specific subunits. Modrich, P., Richardson, C.C. J. Biol. Chem. (1975) [Pubmed]
  14. Beta-L-thymidine 5'-triphosphate analogs as DNA polymerase substrates. Van Draanen, N.A., Tucker, S.C., Boyd, F.L., Trotter, B.W., Reardon, J.E. J. Biol. Chem. (1992) [Pubmed]
  15. Kinetics of nucleotide incorporation opposite polycyclic aromatic hydrocarbon-DNA adducts by processive bacteriophage T7 DNA polymerase. Zang, H., Harris, T.M., Guengerich, F.P. Chem. Res. Toxicol. (2005) [Pubmed]
  16. A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor. Hamdan, S.M., Marintcheva, B., Cook, T., Lee, S.J., Tabor, S., Richardson, C.C. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  17. Replication of duplex DNA by bacteriophage T7 DNA polymerase and gene 4 protein is accompanied by hydrolysis of nucleoside 5'-triphosphates. Kolodner, R., Richardson, C.C. Proc. Natl. Acad. Sci. U.S.A. (1977) [Pubmed]
  18. Error-prone replication of repeated DNA sequences by T7 DNA polymerase in the absence of its processivity subunit. Kunkel, T.A., Patel, S.S., Johnson, K.A. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  19. Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis. Dutta, S., Li, Y., Johnson, D., Dzantiev, L., Richardson, C.C., Romano, L.J., Ellenberger, T. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  20. Thioredoxin and related proteins in procaryotes. Gleason, F.K., Holmgren, A. FEMS Microbiol. Rev. (1988) [Pubmed]
  21. Characterization of bacteriophage T7 DNA polymerase purified to homogeneity by antithioredoxin immunoadsorbent chromatography. Nordström, B., Randahl, H., Slaby, I., Holmgren, A. J. Biol. Chem. (1981) [Pubmed]
  22. Exchange of DNA polymerases at the replication fork of bacteriophage T7. Johnson, D.E., Takahashi, M., Hamdan, S.M., Lee, S.J., Richardson, C.C. Proc. Natl. Acad. Sci. U.S.A. (2007) [Pubmed]
  23. DNA-thumb interactions and processivity of T7 DNA polymerase in comparison to yeast polymerase eta. Cannistraro, V.J., Taylor, J.S. J. Biol. Chem. (2004) [Pubmed]
  24. A molecular handoff between bacteriophage T7 DNA primase and T7 DNA polymerase initiates DNA synthesis. Kato, M., Ito, T., Wagner, G., Ellenberger, T. J. Biol. Chem. (2004) [Pubmed]
  25. The effect of the T7 and Escherichia coli DNA-binding proteins at the replication fork of bacteriophage T7. Nakai, H., Richardson, C.C. J. Biol. Chem. (1988) [Pubmed]
  26. Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis. Tabor, S., Richardson, C.C. J. Biol. Chem. (1989) [Pubmed]
  27. Initiation of DNA replication at the primary origin of bacteriophage T7 by purified proteins. Site and direction of initial DNA synthesis. Fuller, C.W., Richardson, C.C. J. Biol. Chem. (1985) [Pubmed]
  28. Bacteriophage T7 DNA replication. Synthesis of lagging strands in a reconstituted system using purified proteins. Engler, M.J., Richardson, C.C. J. Biol. Chem. (1983) [Pubmed]
  29. Bacteriophage T7 defective in the gene 6 exonuclease promotes site-specific cleavages of T7 DNA in vivo and in vitro. Lee, D.D., Sadowski, P.D. J. Virol. (1982) [Pubmed]
  30. Initiation of DNA replication at the primary origin of bacteriophage T7 by purified proteins: requirement for T7 RNA polymerase. Romano, L.J., Tamanoi, F., Richardson, C.C. Proc. Natl. Acad. Sci. U.S.A. (1981) [Pubmed]
  31. Acidic carboxyl-terminal domain of gene 2.5 protein of bacteriophage T7 is essential for protein-protein interactions. Kim, Y.T., Richardson, C.C. J. Biol. Chem. (1994) [Pubmed]
  32. The linker region between the helicase and primase domains of the bacteriophage T7 gene 4 protein is critical for hexamer formation. Guo, S., Tabor, S., Richardson, C.C. J. Biol. Chem. (1999) [Pubmed]
  33. Interactions of the DNA polymerase and gene 4 protein of bacteriophage T7. Protein-protein and protein-DNA interactions involved in RNA-primed DNA synthesis. Nakai, H., Richardson, C.C. J. Biol. Chem. (1986) [Pubmed]
 
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