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Science 24 June 1994:
Vol. 264. no. 5167, pp. 1891 - 1903
DOI: 10.1126/science.7516580
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Articles

Science, Vol 264, Issue 5167, 1891-1903
Copyright © 1994 by American Association for the Advancement of Science

articles

Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP

H Pelletier, MR Sawaya, A Kumar, SH Wilson, and J Kraut

Department of Chemistry, University of California, San Diego 92093-0317.

Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.


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J. D. Kelly, A. Inga, F.-X. Chen, P. Dande, D. Shah, P. Monti, A. Aprile, P. A. Burns, G. Scott, A. Abbondandolo, et al. (1999)
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Y. CANITROT, M. FRÉCHET, L. SERVANT, C. CAZAUX, and J.-S. HOFFMANN (1999)
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K.-P. Hopfner, A. Eichinger, R. A. Engh, F. Laue, W. Ankenbauer, R. Huber, and B. Angerer (1999)
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W. P. Osheroff, H. K. Jung, W. A. Beard, S. H. Wilson, and T. A. Kunkel (1999)
J. Biol. Chem. 274, 3642-3650
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J. L. Kosa and J. B. Sweasy (1999)
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S. Rajendran, M. J. Jezewska, and W. Bujalowski (1998)
J. Biol. Chem. 273, 31021-31031
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Selective Inhibition of HIV-1 Reverse Transcriptase by an Antiviral Inhibitor, (R)-9-(2-Phosphonylmethoxypropyl)adenine.
Z. Suo and K. A. Johnson (1998)
J. Biol. Chem. 273, 27250-27258
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Mutations Uncover a Role for Two Magnesium Ions in the Catalytic Mechanism of Adenylyl Cyclase.
G. Zimmermann, D. Zhou, and R. Taussig (1998)
J. Biol. Chem. 273, 19650-19655
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An Integrated Model of the Transcription Complex in Elongation, Termination, and Editing.
P. H. von Hippel (1998)
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A Chemical and Genetic Approach Together Define the Biological Consequences of 3-Methyladenine Lesions in the Mammalian Genome.
B. P. Engelward, J. M. Allan, A. J. Dreslin, J. D. Kelly, M. M. Wu, B. Gold, and L. D. Samson (1998)
J. Biol. Chem. 273, 5412-5418
   Abstract »    Full Text »    PDF »
Photoaffinity Labeling by 4-Thiodideoxyuridine Triphosphate of the HIV-1 Reverse Transcriptase Active Site during Synthesis. SEQUENCE OF THE UNIQUE LABELED HEXAPEPTIDE.
S. Lin, W. J. Henzel, S. Nayak, and D. Dennis (1998)
J. Biol. Chem. 273, 997-1002
   Abstract »    Full Text »    PDF »
Characterization of an African Swine Fever Virus 20-kDa DNA Polymerase Involved in DNA Repair.
M. Oliveros, R. J. Yanez, M. L. Salas, J. Salas, E. Vinuela, and L. Blanco (1997)
J. Biol. Chem. 272, 30899-30910
   Abstract »    Full Text »    PDF »
A variant of DNA polymerase beta  acts as a dominant negative mutant.
N. Bhattacharyya and S. Banerjee (1997)
PNAS 94, 10324-10329
   Abstract »    Full Text »    PDF »
One of Two NTP Binding Sites in Poliovirus RNA Polymerase Required for RNA Replication.
O. C. Richards and E. Ehrenfeld (1997)
J. Biol. Chem. 272, 23261-23264
   Abstract »    Full Text »    PDF »
Replication of Template-Primers Containing Propanodeoxyguanosine by DNA Polymerase beta . INDUCTION OF BASE PAIR SUBSTITUTION AND FRAMESHIFT MUTATIONS BY TEMPLATE SLIPPAGE AND DEOXYNUCLEOSIDE TRIPHOSPHATE STABILIZATION.
M. F. Hashim, N. Schnetz-Boutaud, and L. J. Marnett (1997)
J. Biol. Chem. 272, 20205-20212
   Abstract »    Full Text »    PDF »
Base Miscoding and Strand Misalignment Errors by Mutator Klenow Polymerases with Amino Acid Substitutions at Tyrosine 766in the O Helix of the Fingers Subdomain.
J. B. Bell, K. A. Eckert, C. M. Joyce, and T. A. Kunkel (1997)
J. Biol. Chem. 272, 7345-7351
   Abstract »    Full Text »    PDF »


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