Structural and mechanistic relationships between nucleic acid polymerases.

A superfamily of nucleic acid polymerases that includes the pol I and pol alpha classes of DNA-directed DNA polymerases, mitochondrial and phage DNA-directed RNA polymerases, and most RNA-directed polymerases may be defined on the basis of the occurrence of conserved sequence motifs and tertiary structure similarities between HIV-1 reverse transcriptase, DNA polymerase I and T7 RNA polymerase. Although sequence or structural similarities do not yet justify inclusion of the multi-subunit DNA-directed RNA polymerases in this superfamily, mechanistic similarities suggest a deep relationship between these and the simpler T7-like RNA polymerases.

[1]  S. Darst,et al.  Three-dimensional structure of E. coil core RNA polymerase: Promoter binding and elongation conformations of the enzyme , 1995, Cell.

[2]  R. Kornberg,et al.  Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography , 1989, Nature.

[3]  Samuel H. Wilson,et al.  Structure/function studies of human immunodeficiency virus type 1 reverse transcriptase. Alanine scanning mutagenesis of an alpha-helix in the thumb subdomain. , 1994, The Journal of biological chemistry.

[4]  R. Sousa,et al.  A mutant T7 RNA polymerase as a DNA polymerase. , 1995, The EMBO journal.

[5]  J. Gralla,et al.  Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter. , 1980, Biochemistry.

[6]  D. Stuart,et al.  High resolution structures of HIV-1 RT from four RT-inhibitor complexes. , 1996 .

[7]  Seth A. Darst,et al.  Three-dimensional structure of yeast RNA polymerase II at 16 Å resolution , 1991, Cell.

[8]  Yong Je Chung,et al.  Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution , 1993, Nature.

[9]  G. Painter,et al.  Identification of the nucleotide binding site of HIV-1 reverse transcriptase using dTTP as a photoaffinity label. , 1993, Biochemistry.

[10]  Richard I. Gumport,et al.  Transcription termination by bacteriophage T7 RNA polymerase at rho-independent terminators. , 1990, The Journal of biological chemistry.

[11]  M A Mortin,et al.  Molecular modeling of RNA polymerase II mutations onto DNA polymerase I. , 1994, Journal of molecular biology.

[12]  A. Sentenac,et al.  Three‐dimensional model of yeast RNA polymerase I determined by electron microscopy of two‐dimensional crystals. , 1993, The EMBO journal.

[13]  T. Steitz,et al.  Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli. , 1990, The Journal of biological chemistry.

[14]  T. Steitz,et al.  Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. , 1993, Biochemistry.

[15]  T. Steitz,et al.  Function and structure relationships in DNA polymerases. , 1994, Annual review of biochemistry.

[16]  Chris Sander,et al.  DNA polymerase β belongs to an ancient nucleotidyltransferase superfamily , 1995 .

[17]  M. Chamberlin,et al.  RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. , 1989, Biochemistry.

[18]  W. Mcallister,et al.  Substitution of a single bacteriophage T3 residue in bacteriophage T7 RNA polymerase at position 748 results in a switch in promoter specificity. , 1992, Journal of molecular biology.

[19]  R. Gumport,et al.  Transcription termination in vitro by bacteriophage T7 RNA polymerase. The role of sequence elements within and surrounding a rho-independent transcription terminator. , 1992, The Journal of biological chemistry.

[20]  Samuel H. Wilson,et al.  Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. , 1994, Science.

[21]  Samuel H. Wilson,et al.  Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. , 1994, Science.

[22]  V. Sandig,et al.  A phage T7 class-III promoter functions as a polymerase II promoter in mammalian cells. , 1993, Gene.

[23]  M. Chamberlin,et al.  Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Deoxyribonuclease I footprinting of defined complexes. , 1992, Journal of molecular biology.

[24]  W. Mcallister,et al.  Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon a three base-pair region located 10 to 12 base-pairs upstream from the start site. , 1990, Journal of molecular biology.

[25]  T. Steitz,et al.  A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. , 1994, Science.

[26]  H. Heumann,et al.  The 'helix clamp' in HIV-1 reverse transcriptase: a new nucleic acid binding motif common in nucleic acid polymerases. , 1994, Nucleic acids research.

[27]  C. M. Joyce,et al.  Deoxynucleoside Triphosphate and Pyrophosphate Binding Sites in the Catalytically Competent Ternary Complex for the Polymerase Reaction Catalyzed by DNA Polymerase I (Klenow Fragment) (*) , 1995, The Journal of Biological Chemistry.

[28]  A. Woody,et al.  Bacteriophage T7 RNA polymerase and its active-site mutants. Kinetic, spectroscopic and calorimetric characterization. , 1994, Journal of molecular biology.

[29]  T. Steitz,et al.  Structure of DNA polymerase I Klenow fragment bound to duplex DNA , 1993, Science.

[30]  D. Patra,et al.  Model for the mechanism of bacteriophage T7 RNAP transcription initiation and termination. , 1992, Journal of molecular biology.

[31]  A. D. Clark,et al.  Insights into DNA polymerization mechanisms from structure and function analysis of HIV-1 reverse transcriptase. , 1995, Biochemistry.

[32]  D. Patra,et al.  Isolation and characterization of mutant bacteriophage T7 RNA polymerases. , 1992, Journal of molecular biology.

[33]  W R McClure,et al.  Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes. , 1980, The Journal of biological chemistry.

[34]  Jianping Ding,et al.  Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance. , 1994, Journal of molecular biology.

[35]  P Argos,et al.  An attempt to unify the structure of polymerases. , 1990, Protein engineering.

[36]  M. Chamberlin,et al.  Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators. , 1992, Journal of molecular biology.

[37]  T. Steitz,et al.  Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. , 1992, Science.

[38]  M. Wainberg,et al.  Monoclonal antibody-mediated inhibition of HIV-1 reverse transcriptase polymerase activity. Interaction with a possible deoxynucleoside triphosphate binding domain. , 1993, Journal of Biological Chemistry.

[39]  A. D. Clark,et al.  Structure of HIV-1 reverse transcriptase/DNA complex at 7 Å resolution showing active site locations , 1992, Nature.

[40]  C. Martin,et al.  Processivity in early stages of transcription by T7 RNA polymerase. , 1988, Biochemistry.

[41]  W. Mcallister,et al.  Identification of a region of the bacteriophage T3 and T7 RNA polymerases that determines promoter specificity. , 1990, Journal of molecular biology.

[42]  P. Farnham,et al.  A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs , 1980, Cell.

[43]  A. D. Clark,et al.  Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[44]  I Sauvaget,et al.  Identification of four conserved motifs among the RNA‐dependent polymerase encoding elements. , 1989, The EMBO journal.

[45]  J. Jaehning,et al.  Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. , 1994, The Journal of biological chemistry.

[46]  S. Benkovic,et al.  Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. , 1992, The Journal of biological chemistry.