4ISJ

RNA Ligase RtcB in complex with Mn(II)

4ISJ の概要

• エントリーDOI: 10.2210/pdb4isj/pdb
• 関連するPDBエントリー: 4ISZ 4IT0
• 関連するBIRD辞書のPRD_ID: PRD_900003
• 分子名称: tRNA-splicing ligase RtcB, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, MANGANESE (II) ION, ... (5 entities in total)
• 機能のキーワード: rna ligase, ligase
• 由来する生物種: Pyrococcus horikoshii; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 109208.13

構造登録者

Desai, K.K.,Bingman, C.A.,Phillips Jr., G.N.,Raines, R.T. (登録日: 2013-01-16, 公開日: 2013-03-20, 最終更新日: 2024-02-28)

主引用文献

Desai, K.K.,Bingman, C.A.,Phillips, G.N.,Raines, R.T.
Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation.
Biochemistry, 52:2518-2525, 2013

PubMed Abstract: RtcB is an atypical RNA ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. In contrast to typical RNA ligases, which rely on ATP and Mg(II), catalysis by RtcB is dependent on GTP and Mn(II) with ligation proceeding through a covalent RtcB-histidine-GMP intermediate. Here, we present three structures of Pyrococcus horikoshii RtcB complexes that capture snapshots along the entire guanylylation pathway. These structures show that prior to binding GTP, a single manganese ion (Mn1) is bound to RtcB. To capture the step immediately preceding RtcB guanylylation, we determined a structure of RtcB in complex with Mn(II) and the unreactive GTP analogue guanosine 5'-(α-thio)triphosphate (GTPαS). This structure shows that Mn1 is poised to stabilize the pentavalent transition state of guanylylation while a second manganese ion (Mn2) is coordinated to a nonbridging oxygen of the γ-phosphoryl group. The pyrophosphate leaving group of GTPαS is oriented apically to His404 with the ε-nitrogen poised for in-line attack on the α-phosphorus atom. The structure of RtcB in complex with GTPαS also reveals the network of hydrogen bonds that recognize GTP and illuminates the significant conformational changes that accompany the binding of this cofactor. Finally, a structure of the enzymic histidine-GMP intermediate depicts the end of the guanylylation pathway. The ensuing molecular description of the RtcB guanylylation pathway shows that RtcB and classical ATP- and Mg(II)-dependent nucleic acid ligases have converged upon a similar two-metal mechanism for formation of the nucleotidylated enzyme intermediate.

PubMed: 23560983
DOI: 10.1021/bi4002375

実験手法

X-RAY DIFFRACTION (2.344 Å)