3W34

Ternary complex of Thermus thermophilus HB8 uridine-cytidine kinase with substrates

3W34 の概要

• エントリーDOI: 10.2210/pdb3w34/pdb
• 分子名称: Uridine kinase, 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE, PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER, ... (4 entities in total)
• 機能のキーワード: kinase, nucleoside, transferase
• 由来する生物種: Thermus thermophilus
• 細胞内の位置: Cytoplasm : Q5SKR5
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 48916.30

構造登録者

Tomoike, F.,Nakagawa, N.,Masui, R.,Kuramitsu, S. (登録日: 2012-12-10, 公開日: 2013-12-11, 最終更新日: 2024-03-20)

主引用文献

Tomoike, F.,Nakagawa, N.,Kuramitsu, S.,Masui, R.
Structural and Biochemical Studies on the Reaction Mechanism of Uridine-Cytidine Kinase
Protein J., 34:411-420, 2015

PubMed Abstract: Uridine-cytidine kinase catalyzes phosphorylation of the pyrimidine nucleosides uridine and cytidine and plays an important role in nucleotide metabolism. However, the detailed molecular mechanism of these reactions remains to be elucidated. Here, we determined the structure of the ternary complex of Uridine-cytidine kinase from Thermus thermophilus HB8 with both cytidine and β,γ-methyleneadenosine 5'-triphosphate, a non-hydrolysable ATP analogue. Substrate binding is accompanied by substantial domain movement that allows the substrate-binding cleft to close. The terminal phosphodiester bond of the ATP analogue is in an ideal location for an inline attack of the 5'-hydroxyl group of cytidine. Asp40 is located near the 5'-hydroxyl group of cytidine. Mutation of this conserved residue to Asn or Ala resulted in a complete loss of enzyme activity, which is consistent with the notion that Asp40 acts as a general base that activates the 5'-hydroxyl group of cytidine. The pH profile of the activity showed an apparent pK a value of 7.4. Based on this structure, a likely mechanism of the catalytic step is discussed.

PubMed: 26510656
DOI: 10.1007/s10930-015-9636-8

実験手法

X-RAY DIFFRACTION (1.91 Å)