Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus

@article{Aihara2016StructuralAF,
  title={Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus},
  author={Takayuki Aihara and Toshiya Ito and Yasuaki Yamanaka and Keiichi Noguchi and Masafumi Odaka and Masae Sekine and Hiroshi Homma and Masafumi Yohda},
  journal={Extremophiles},
  year={2016},
  volume={20},
  pages={385-393}
}
Functional and structural characterizations of pyridoxal 5′-phosphate-independent aspartate racemase of the acidothermophilic archaeon Picrophilus torridus were performed. Picrophilus aspartate racemase exhibited high substrate specificity to aspartic acid. The optimal reaction temperature was 60 °C, which is almost the same as the optimal growth temperature. Reflecting the low pH in the cytosol, the optimal reaction pH of Picrophilus aspartate racemase was approximately 5.5. However, the… 
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References

SHOWING 1-10 OF 22 REFERENCES
Gene for Aspartate Racemase from the Sulfur-dependent Hyperthermophilic Archaeum, Desulfurococcus Strain SY*
TLDR
The cloned protein had amino acid racemizing activity, which was highly specific for aspartate and increased with temperature from 37°C to 90°C, and was identified as the first hyperthermophilic archaeal amino Acid racemase.
Properties of aspartate racemase, a pyridoxal 5'-phosphate-independent amino acid racemase.
Occurrence of D-Amino Acids and a pyridoxal 5'-phosphate-dependent aspartate racemase in the acidothermophilic archaeon, Thermoplasma acidophilum.
TLDR
Free D-amino acid content in some archaea was investigated and D-forms of several amino acids were found in them, finding that high levels of d-Asp should be produced by a new type(s) of Asp-specific racemase in Thermoplasma acidophilum, although the function of d -Asp in this archaeon remains unknown.
Distribution and purification of aspartate racemase in lactic acid bacteria.
Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism
TLDR
The crystal structure of an inactive mutant PhAspR complexed with a citric acid (Cit) at a resolution of 2.0 Å is determined, which reveals a pseudo mirror‐symmetric distribution of the residues around its active site, which is very reasonable for its chiral substrates, L‐ aspartate and D‐aspartate.
Identification of a novel amino acid racemase from a hyperthermophilic archaeon Pyrococcus horikoshii OT-3 induced by d-amino acids
TLDR
It is found that the hyperthermophilic archaeon Pyrococcus horikoshii OT-3 requires Thr, Leu, Val, Phe, Tyr, Trp, His and Arg in the medium for growth, and shows slow growth in medium lacking Met or Ile.
Occurrence of Free d-Amino Acids and Aspartate Racemases in Hyperthermophilic Archaea
TLDR
It is proven that D-amino acids are produced in some hyperthermophilic archaea, although their function is unknown, and they might be by-products of aspartate racemase.
Roles of conserved basic amino acid residues and activation mechanism of the hyperthermophilic aspartate racemase at high temperature
TLDR
Insight is provided into the roles of amino acid residues at the catalytic site and the activation mechanism of a hyperthermophilic aspartate racemase at high temperature and the distance between the two active γ‐sulfur atoms of cysteine residues oscillate to periodically become shorter than the predicted cooperative distance at highTemperature.
Genome sequence of Picrophilus torridus and its implications for life around pH 0
TLDR
It is noteworthy that the thermoacidophiles from phylogenetically distant branches of the Archaea apparently share an unexpectedly large pool of genes.
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