Role of conserved amino acids in the catalytic activity of Escherichia coli primase

Journal of Bacteriology

Volumn 188, Issue 10, 2006, Pages 3614-3621

  Rodina, Anna ^a,c   Godson, G Nigel ^a,b  

^a NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ASPARTIC ACID; DNA PRIMASE; GLYCINE; LYSINE; METHIONINE; TYROSINE;

AMINO ACID METABOLISM; AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; DNA REPLICATION; ENZYME STABILITY; GENETIC CONSERVATION; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SYNTHESIS;

AMINO ACID SEQUENCE; BASE SEQUENCE; CONSERVED SEQUENCE; DNA PRIMASE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; OLIGODEOXYRIBONUCLEOTIDES; RNA, BACTERIAL;

ESCHERICHIA COLI;

EID: 33646552062     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.188.10.3614-3621.2006     Document Type: Article

References (26)

1. Aravind, L., D. D. Leipe, and E. V. Koonin. 1998. Toprim-a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res. 26:4205-4213.
2. Bouche, J. P., L. Rowen, and A. Kornberg. 1978. The RNA primer synthesized by primase to initiate phage G4 DNA replication. J. Biol. Chem. 253:765-769.
3. Copeland, W. C., and T. S. Wang. 1993. Mutational analysis of the human DNA polymerase alpha. The most conserved region in alpha-like DNA polymerases is involved in metal-specific catalysis. J. Biol. Chem. 268:11028-11040.
4. Crouch, E., S. Miller, V. Wilson, and D. Busbee. 1997. A DNA polymerase alpha accessory protein exhibits structural and functional similarities to SV40 large tumor antigen. Mutat. Res. 374:109-123.
5. Frick, D. N., and C. C. Richardson. 2001. DNA primases. Annu. Rev. Biochem. 70:39-80.
6. Godson, G. N. 1991. An over-expression plasmid for Escherichia coli primase. Gene 100:59-64.
7. Godson, G. N., J. Schoenich, W. Sun, and A. A. Mustaev. 2000. Identification of the magnesium ion binding site in the catalytic center of Escherichia coli primase by iron cleavage. Biochemistry 39:332-339.
8. Higuchi, R. 1990. Recombinant PCR, p. 177-183. In M. A. Innis, D. H. Gelfand, J. J. Snisky, and T. J. White (ed.), PCR protocols. A guide to methods and applications. Academic Press, New York, N.Y.
9. Ilyina, T. V., A. E. Gorbalenya, and E. V. Koonin. 1992. Organization and evolution of bacterial and bacteriophage primase-helicase systems. J. Mol. Evol. 34:351-357.
10. Keck, J. L., D. D. Roche, A. S. Lynch, and J. M. Berger. 2000. Structure of the RNA polymerase domain of E. coli primase. Science 287:2482-2486.
11. Kitani, T., K. Yoda, T. Ogawa, and T. Okazaki. 1985. Evidence that discontinuous DNA replication in Escherichia coli is primed by approximately 10 to 12 residues of RNA starting with a purine. J. Mol. Biol. 184:45-52.
12. Kornberg, A., and T. A. Baker. 1992. DNA replication, 2nd ed. Freeman, New York, N.Y.
13. Korzheva, N., A. Mustaev, E. Nudler, V. Nikiforov, and A. Goldfarb. 1998. Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. Cold Spring Harbor Symp. Quant. Biol. 63:337-345.
14. Nudler, E. 1999. Transcription elongation: structural basis and mechanisms. J. Mol. Biol. 288:1-12.
15. Podobnik, M., P. McInerney, M. O'Donnell, and L. Kuriyan. 2000. A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases. J. Mol. Biol. 300:353-362.
16. Pritchard, A. E., and C. S. McHenry. 1999. Identification of the acidic residues in the active site of DNA polymerase III. J. Mol. Biol. 285:1067-1080.
17. Saturno, J., J. M. Lazaro, L. Blanco, and M. Salas. 1998. Role of the first aspartate residue of the "YxDTDS" motif of phi29 DNA polymerase as a metal ligand during both TP-primed and DNA-primed DNA synthesis. J. Mol. Biol. 283:633-642.
18. Sheaff, R. J., and R. D. Kuchta. 1993. Mechanism of calf thymus DNA primase: slow initiation, rapid polymerization, and intelligent termination. Biochemistry 32:3027-3037.
19. Strack, B., M. Lessl, R. Calendar, and E. Lanka. 1992. A common sequence motif, -E-G-Y-A-T-A-, identified within the primase domains of plasmid-encoded I- and P-type DNA primases and the alpha protein of the Escherichia coli satellite phage P4. J. Biol. Chem. 267:13062-13072.
20. c-E. coli SSB complex. J. Bacteriol. 178:6701-6705.
21. Sun, W., and G. N. Godson. 1998. Synthesis of polyribonucleotide chains from the 3′-hydroxyl terminus of oligodeoxynucleotides by Escherichia coli primase. J. Biol. Chem. 273:16358-16365.
22. Sun, W., J. Schoneich, and G. N. Godson. 1999. A mutant Escherichia coli primase defective in elongation of primer RNA chains. J. Bacteriol. 181:3761-3767.
23. Sun, W., J. Tormo, T. A. Steitz, and G. N. Godson. 1994. Domains of Escherichia coli primase: functional activity of a 47-kDa N-terminal proteolytic fragment. Proc. Natl. Acad. Sci. USA 91:11462-11466.
24. Szafranski, P., C. L. Smith, and C. R. Cantor. 1997. Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase. Biochim. Biophys. Acta 1352:243-248.
25. Washington, M. T., A. H. Rosenberg, K. Griffin, F. W. Studier, and S. S. Patel. 1996. Biochemical analysis of mutant T7 primase/helicase proteins defective in DNA binding, nucleotide hydrolysis, and the coupling of hydrolysis with DNA unwinding. J. Biol. Chem. 271:26825-26834.
26. Yong, Y., and L. J. Romano. 1995. Nucleotide and DNA-induced conformational changes in the bacteriophage T7 gene 4 protein. J. Biol. Chem. 270:24509-24517.