Helix–hairpin–helix motifs confer salt resistance and processivity on chimeric DNA polymerases

@article{Pavlov2002HelixhairpinhelixMC,
  title={Helix–hairpin–helix motifs confer salt resistance and processivity on chimeric DNA polymerases},
  author={Andrey R. Pavlov and Galina I. Belova and Sergei A. Kozyavkin and Alexei I. Slesarev},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2002},
  volume={99},
  pages={13510 - 13515}
}
Helix–hairpin–helix (HhH) is a widespread motif involved in sequence-nonspecific DNA binding. The majority of HhH motifs function as DNA-binding modules with typical occurrence of one HhH motif or one or two (HhH)2 domains in proteins. We recently identified 24 HhH motifs in DNA topoisomerase V (Topo V). Although these motifs are dispensable for the topoisomerase activity of Topo V, their removal narrows the salt concentration range for topoisomerase activity tenfold. Here, we demonstrate the… 

Figures from this paper

Chimeric Phi29 DNA polymerase with helix–hairpin–helix motifs shows enhanced salt tolerance and replication performance
TLDR
The multiple advantages of (HhH)2 domain insertion make it a good substitute for Phi29 Pol, especially for use in nanopore sequencing or other circumstances that require high salt concentrations, as well as ionic, current‐based sequencing technology.
Improvement of φ29 DNA polymerase amplification performance by fusion of DNA binding motifs
TLDR
The chimerical DNA polymerases display an improved and faithful multiply primed DNA amplification proficiency on both circular plasmids and genomic DNA and are unique φ29 DNA polymerase variants with enhanced amplification performance.
Enhancing the processivity of a family B-type DNA polymerase of Thermococcus onnurineus and application to long PCR
TLDR
N213D mutant protein had higher processivity and extension rate than the wild-type TNA1 DNA polymerase, retaining a lower mutation frequency than recombinant TaqDNA polymerase.
Cooperation between catalytic and DNA binding domains enhances thermostability and supports DNA synthesis at higher temperatures by thermostable DNA polymerases.
TLDR
It is found that reversible high-temperature structural transitions in DNA polymerases decrease the rates of binding of these enzymes to the templates, and activation energies and pre-exponential factors of the Arrhenius equation suggest that the mechanism of electrostatic enhancement of diffusion-controlled association plays a minor role in binding of templates to DNA polymerase.
DNA-Binding Domain of DNA Ligase from the Thermophilic Archaeon Pyrococcus abyssi: Improving Long-Range PCR and Neutralization of Heparin’s Inhibitory Effect
TLDR
Inclusion of the C-terminally 6X His-tagged PabDBD in the reaction mixture during long-range polymerase chain reaction (PCR) increased the efficacy of amplification and eliminated the inhibitory effect of heparin.
Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix
TLDR
This study has enhanced salt tolerance of bovine DNaseI and successfully mimicked the Nature’s evolutionary engineering that created the extremely halotolerant bacterial DNase.
Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism
TLDR
The structures of topoisomerase V in complex with DNA show a DNA binding mode not observed before and provide information on the way this unusual topoisomersase relaxes DNA.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 24 REFERENCES
The helix-hairpin-helix DNA-binding motif: a structural basis for non- sequence-specific recognition of DNA
TLDR
One, two or four copies of the 'helix-hairpin-helix' (HhH) DNA-binding motif are predicted to occur in 14 homologous families of proteins, and it is suggested that each of these HhH motifs bind DNA in a non-sequence-specific manner, via the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups.
Common fold in helix-hairpin-helix proteins.
TLDR
This analysis helps to clarify how non-symmetric protein motifs bind to the double helix of DNA through the formation of a pseudo-2-fold symmetric (HhH)(2) functional unit.
The Domain Organization and Properties of Individual Domains of DNA Topoisomerase V, a Type 1B Topoisomerase with DNA Repair Activities*
TLDR
Topo V has at least two active sites capable of processing AP DNA, and it is demonstrated that Topo78 and Topo34 possess AP lyase activities that are important in base excision DNA repair.
Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
TLDR
The crystal structure of endonuclease III, combined with mutational analysis, suggests the structural basis for the DNA binding and catalytic activity of the enzyme and identifies Helix‐hairpin‐helix and FCL motifs, which may be a recurrent structural theme for DNA binding proteins.
Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity.
TLDR
Crystal structures of human pol beta complexed with blunt-ended segments of DNA show that, although the crystals belong to a different space group, the DNA is nevertheless bound in the pol beta binding channel in the same way as the DNA in previously reported structures of rat pol beta complexes with a template-primer and ddCTP.
Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation.
  • Y. Li, V. Mitaxov, G. Waksman
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1999
TLDR
The crystal structures of all four ddNTP-trapped closed ternary complexes of the large fragment of the Taq DNA polymerase (Klentaq1) are determined, resulting in a significant improvement in the accuracy of DNA sequencing.
A type IB topoisomerase with DNA repair activities
TLDR
Topo V is the prototype for a new subfamily of type IB topoisomersases and is the first example of a topoisomerase with associated DNA repair activities.
DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote
TLDR
The findings support the idea that some essential parts of the eukaryotic transcription–translation and replication machineries were in place before the emergence of eukARYotes, and that the closest living relatives of eUKaryotes may be hyperthermophiles.
Domain exchange: chimeras of Thermus aquaticus DNA polymerase, Escherichia coli DNA polymerase I and Thermotoga neapolitana DNA polymerase.
TLDR
The chimera TaqEc1 showed characteristics from both parental polymerases at an intermediate temperature of 50 degrees C: high polymerase activity, processivity, 3'-5' exonuclease activity and proof-reading function.
...
1
2
3
...