5X0K

Free serine kinase (E30Q mutant) in complex with AMP

5X0K の概要

• エントリーDOI: 10.2210/pdb5x0k/pdb
• 関連するPDBエントリー: 5X0B 5X0E 5X0F 5X0G 5X0J
• 分子名称: Free serine kinase, ADENOSINE MONOPHOSPHATE (3 entities in total)
• 機能のキーワード: thermococcus kodakarensis, cysteine biosynthesis, transferase
• 由来する生物種: Thermococcus kodakarensis KOD1
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 28085.25

構造登録者

Nagata, R.,Fujihashi, M.,Miki, K. (登録日: 2017-01-20, 公開日: 2017-04-12, 最終更新日: 2023-11-22)

主引用文献

Nagata, R.,Fujihashi, M.,Kawamura, H.,Sato, T.,Fujita, T.,Atomi, H.,Miki, K.
Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis
ACS Chem. Biol., 12:1514-1523, 2017

PubMed Abstract: 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.

PubMed: 28358477
DOI: 10.1021/acschembio.7b00064

実験手法

X-RAY DIFFRACTION (1.65 Å)