8DCB

RNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ and GTP

8DCB の概要

• エントリーDOI: 10.2210/pdb8dcb/pdb
• 関連するPDBエントリー: 8DC9
• 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, GUANOSINE-5'-TRIPHOSPHATE, ... (8 entities in total)
• 機能のキーワード: rtcb, rna ligase, trna splicing, rna repair, ligase
• 由来する生物種: Pyrococcus horikoshii OT3; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 114655.61

構造登録者

Jacewicz, A.,Dantuluri, S.,Shuman, S. (登録日: 2022-06-16, 公開日: 2022-10-12, 最終更新日: 2023-10-18)

主引用文献

Jacewicz, A.,Dantuluri, S.,Shuman, S.
Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
Rna, 28:1509-1518, 2022

PubMed Abstract: (Pho) RtcB exemplifies a family of binuclear transition metal- and GTP-dependent RNA ligases that join 3'-phosphate and 5'-OH ends via RtcB-(histidinyl-N)-GMP and RNAppG intermediates. We find that guanylylation of PhoRtcB is optimal with manganese and less effective with cobalt and nickel. Zinc and copper are inactive and potently inhibit manganese-dependent guanylylation. We report crystal structures of PhoRtcB in complexes with GTP and permissive (Mn, Co, Ni) or inhibitory (Zn, Cu) metals. Zinc and copper occupy the M1 and M2 sites adjacent to the GTP phosphates, as do manganese, cobalt, and nickel. The identity/positions of enzymic ligands for M1 (His234, His329, Cys98) and M2 (Cys98, Asp95, His203) are the same for permissive and inhibitory metals. The differences pertain to: (i) the coordination geometries and phosphate contacts of the metals; and (ii) the orientation of the His404 nucleophile with respect to the GTP α-phosphate and pyrophosphate leaving group. M2 metal coordination geometry correlates with metal cofactor activity, whereby inhibitory Zn2 and Cu2 assume a tetrahedral configuration and contact only the GTP γ-phosphate, whereas Mn2, Co2, and Ni2 coordination complexes are pentahedral and contact the β- and γ-phosphates. The His404-Nε-Pα-O(α-β) angle is closer to apical in Mn (179°), Co (171°), and Ni (169°) structures than in Zn (160°) and Cu (155°) structures. The octahedral Mn1 geometry in our RtcB•GTP•Mn structure, in which Mn1 contacts α-, β-, and γ-phosphates, transitions to a tetrahedral configuration after formation of RtcB•(His404)-GMP•Mn and departure of pyrophosphate.

PubMed: 36130078
DOI: 10.1261/rna.079327.122

実験手法

X-RAY DIFFRACTION (2.6 Å)