Publications

• Structural study on the reaction mechanism of a free serine kinase involved in cysteine biosynthesis.

  Nagata R., Fujihashi M., Kawamura H., Sato T., Fujita T., Atomi H., Miki K.

  A free serine kinase (SerK) is involved in l-cysteine biosynthesis in the hyperthermophilic archaeon Thermococcus kodakarensis. The enzyme converts ADP and l-serine (Ser) into AMP and O-phospho-l-serine (Sep), which is a precursor of l-cysteine. SerK is the first identified enzyme that phosphoryla ... >> More

  A free serine kinase (SerK) is involved in l-cysteine biosynthesis in the hyperthermophilic archaeon Thermococcus kodakarensis. The enzyme converts ADP and l-serine (Ser) into AMP and O-phospho-l-serine (Sep), which is a precursor of l-cysteine. SerK is the first identified enzyme that phosphorylates free serine, while serine/threonine protein kinases have been well studied. SerK displays low sequence similarities to known kinases, suggesting that its reaction mechanism is different from those of known kinases. Here, we determined the crystal structures of SerK from T. kodakarensis (Tk-SerK). The overall structure is divided into two domains. A large cleft is found between the two domains in the AMP complex and in the ADP complex. The cleft is closed in the ternary product complex (Sep, AMP, and Tk-SerK) and may also be in the ternary substrate complex (Ser, ADP, and Tk-SerK). The closure may reorient the carboxyl group of E30 near to the Oγ atom of Ser. The Oγ atom is considered to be deprotonated by E30 and to attack the β-phosphate of ADP to form Sep. The substantial decrease in the activity of the E30A mutant is consistent with this mechanism. Our structures also revealed the residues that contribute to the ligand binding. The conservation of these residues in uncharacterized proteins from bacteria may raise the possibility of the presence of free Ser kinases not only in archaea but also in bacteria. << Less

  ACS Chem. Biol. 12:1514-1523(2017) [PubMed] [EuropePMC]

• An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism.

  Makino Y., Sato T., Kawamura H., Hachisuka S.I., Takeno R., Imanaka T., Atomi H.

  Routes for cysteine biosynthesis are still unknown in many archaea. Here we find that the hyperthermophilic archaeon Thermococcus kodakarensis generates cysteine from serine via O-phosphoserine, in addition to the classical route from 3-phosphoglycerate. The protein responsible for serine phosphor ... >> More

  Routes for cysteine biosynthesis are still unknown in many archaea. Here we find that the hyperthermophilic archaeon Thermococcus kodakarensis generates cysteine from serine via O-phosphoserine, in addition to the classical route from 3-phosphoglycerate. The protein responsible for serine phosphorylation is encoded by TK0378, annotated as a chromosome partitioning protein ParB. The TK0378 protein utilizes ADP as the phosphate donor, but in contrast to previously reported ADP-dependent kinases, recognizes a non-sugar substrate. Activity is specific towards free serine, and not observed with threonine, homoserine and serine residues within a peptide. Genetic analyses suggest that TK0378 is involved in serine assimilation and clearly responsible for cysteine biosynthesis from serine. TK0378 homologs, present in Thermococcales and Desulfurococcales, are most likely not ParB proteins and constitute a group of kinases involved in serine utilization. << Less

  Nat. Commun. 7:13446-13446(2016) [PubMed] [EuropePMC]