4JT2

Structure of Clostridium thermocellum polynucleotide kinase bound to CTP

4JT2 の概要

• エントリーDOI: 10.2210/pdb4jt2/pdb
• 関連するPDBエントリー: 4GP6 4GP7 4JST 4JSY 4JT4
• 分子名称: Metallophosphoesterase, MAGNESIUM ION, CYTIDINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: rna repair, p-loop phosphotransferase, polynucleotide kinase, transferase
• 由来する生物種: Clostridium thermocellum
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 40337.05

構造登録者

Das, U.,Wang, L.K.,Smith, P.,Shuman, S. (登録日: 2013-03-22, 公開日: 2013-08-28, 最終更新日: 2024-11-06)

主引用文献

Das, U.,Wang, L.K.,Smith, P.,Shuman, S.
Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkphen1 RNA repair system.
Biochemistry, 52:4734-4743, 2013

PubMed Abstract: Clostridium thermocellum Pnkp is the end-healing and end-sealing subunit of a bacterial RNA repair system. CthPnkp is composed of three catalytic modules: an N-terminal 5'-OH polynucleotide kinase, a central 2',3' phosphatase, and a C-terminal ligase. The crystal structure of the kinase domain bound to ATP•Mg(2+) revealed a rich network of ionic and hydrogen-bonding contacts to the α, β, and γ phosphates. By contrast, there are no enzymic contacts to the ribose and none with the adenine base other than a π-cation interaction with Arg116. Here we report that the enzyme uses ATP, GTP, CTP, UTP, or dATP as a phosphate donor for the 5'-OH kinase reaction. The enzyme also catalyzes the reverse reaction, in which a polynucleotide 5'-PO4 group is transferred to ADP, GDP, CDP, UDP, or dADP to form the corresponding NTP. We report new crystal structures of the kinase in complexes with GTP, CTP, UTP, and dATP in which the respective nucleobases are stacked on Arg116 but make no other enzymic contacts. Mutating Arg116 to alanine elicits a 10-fold increase in Km for ATP but has little effect on kcat. These findings illuminate the basis for nonspecific donor nucleotide utilization by a P-loop phosphotransferase.

PubMed: 23721485
DOI: 10.1021/bi400412x

実験手法

X-RAY DIFFRACTION (2.49 Å)