Involvement of the “linker” region between the exonuclease and polymerization domains of ϕ29 DNA polymerase in DNA and TP binding

Truniger, Verónica; Bonnin, Ana; Lázaro, José Portolés; Vega, Miguel de; Salas, Margarita

doi:10.1016/j.gene.2004.12.041

Cited by 3 publications

(2 citation statements)

References 37 publications

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“…4a), a sequence that is important for interactions with DNA in the primer-terminal region. 36,37 Thus, the amino acid substitutions for residues at base positions of helices N and P (G466S, L567F) and the substitutions for residues Y460, N582, and A580 appear to link P424 in the NPL core to the fingers domain and to conserved residues that are important for DNA interactions.…”

Section: Resultsmentioning

confidence: 99%

Identification of a New Motif in Family B DNA Polymerases by Mutational Analyses of the Bacteriophage T4 DNA Polymerase

Hogg

Reha-Krantz

2010

Journal of Molecular Biology

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Structure-based protein sequence alignments of family B DNA polymerases revealed a conserved motif that is formed from interacting residues between loops from the N-terminal and palm domains and between the N-terminal loop and a conserved proline residue. The importance of the motif for function of the bacteriophage T4 DNA polymerase was revealed by suppressor analysis. T4 DNA polymerases that form weak replicating complexes cannot replicate DNA when the dGTP pool is reduced. The conditional lethality provides the means to identify amino acid substitutions that restore replication activity under low dGTP conditions by either correcting the defect produced by the first amino acid substitution or by generally increasing the stability of polymerase complexes; the second type are global suppressors that can effectively counter the reduced stability caused by a variety of amino acid substitutions. Some amino acid substitutions that increase the stability of polymerase complexes produce a new phenotype - sensitivity to the antiviral drug phosphonoacetic acid. Amino acid substitutions that confer decreased ability to replicate DNA under low dGTP conditions or drug sensitivity were identified in the new motif, which suggests that the motif functions in regulating the stability of polymerase complexes. Additional suppressor analyses revealed an apparent network of interactions that link the new motif to the fingers domain and to two patches of conserved residues that bind DNA. The collection of mutant T4 DNA polymerases provides a foundation for future biochemical studies to determine how DNA polymerases remain stably associated with DNA while waiting for the next available dNTP, how DNA polymerases translocate, and the biochemical basis for sensitivity to antiviral drugs.

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Section: Resultsmentioning

confidence: 99%

Identification of a New Motif in Family B DNA Polymerases by Mutational Analyses of the Bacteriophage T4 DNA Polymerase

Hogg

Reha-Krantz

2010

Journal of Molecular Biology

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“…1d), indicating that these regions may represent TP precursor(s). Moreover, DpoBa and DpoBb contain an insertion between exonuclease (ExoIII) and polymerase (PolI) domains, reminiscent of the linker domain of the phi29 DNA polymerase important for DNA and TP binding (Truniger et al , 2005). This supports the idea that DpoBa and/or DpoBb may be involved in replication initiation by a protein-priming mechanism.…”

Section: Discussionmentioning

confidence: 99%

The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5′ termini

et al. 2010

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As a part of our initiative aimed at a large-scale comparative analysis of fungal mitochondrial genomes, we determined the complete DNA sequence of the mitochondrial genome of the yeast Candida subhashii and found that it exhibits a number of peculiar features. First, the mitochondrial genome is represented by linear dsDNA molecules of uniform length (29 795 bp), with an unusually high content of guanine and cytosine residues (52.7 %). Second, the coding sequences lack introns; thus, the genome has a relatively compact organization. Third, the termini of the linear molecules consist of long inverted repeats and seem to contain a protein covalently bound to terminal nucleotides at the 5′ ends. This architecture resembles the telomeres in a number of linear viral and plasmid DNA genomes classified as invertrons, in which the terminal proteins serve as specific primers for the initiation of DNA synthesis. Finally, although the mitochondrial genome of C. subhashii contains essentially the same set of genes as other closely related pathogenic Candida species, we identified additional ORFs encoding two homologues of the family B protein-priming DNA polymerases and an unknown protein. The terminal structures and the genes for DNA polymerases are reminiscent of linear mitochondrial plasmids, indicating that this genome architecture might have emerged from fortuitous recombination between an ancestral, presumably circular, mitochondrial genome and an invertron-like element.

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DNA polymerase proofreading: Multiple roles maintain genome stability

Reha-Krantz

2010

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

152

175

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Involvement of the “linker” region between the exonuclease and polymerization domains of ϕ29 DNA polymerase in DNA and TP binding

Cited by 3 publications

References 37 publications

Identification of a New Motif in Family B DNA Polymerases by Mutational Analyses of the Bacteriophage T4 DNA Polymerase

Identification of a New Motif in Family B DNA Polymerases by Mutational Analyses of the Bacteriophage T4 DNA Polymerase

The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5′ termini

DNA polymerase proofreading: Multiple roles maintain genome stability

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