3TUT

Crystal structure of RtcA.ATP binary complex

3TUT の概要

• エントリーDOI: 10.2210/pdb3tut/pdb
• 関連するPDBエントリー: 1QMH 1QMI 3KGD 3TUX 3TV1 3TW3
• 分子名称: RNA 3'-terminal phosphate cyclase, ADENOSINE-5'-TRIPHOSPHATE, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: cyclase family, cyclization of rna 3'-phosphate ends, transferase
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm: P46849
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 39061.93

構造登録者

Chakravarty, A.K.,Smith, P.,Shuman, S. (登録日: 2011-09-18, 公開日: 2011-12-28, 最終更新日: 2023-09-13)

主引用文献

Chakravarty, A.K.,Smith, P.,Shuman, S.
Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.
Proc.Natl.Acad.Sci.USA, 108:21034-21039, 2011

PubMed Abstract: RNA 3'-phosphate cyclase (RtcA) synthesizes RNA 2',3' cyclic phosphate ends via three steps: reaction with ATP to form a covalent RtcA-(histidinyl-Nε)-AMP intermediate; transfer of adenylate to an RNA 3'-phosphate to form RNA(3')pp(5')A; and attack of the vicinal O2' on the 3'-phosphorus to form a 2',3' cyclic phosphate and release AMP. Here we report the crystal structures of RtcA•ATP, RtcA•ATP•Mn(2+), and RtcA•ATP•Co(2+) substrate complexes and an RtcA•AMP product complex. Together with the structures of RtcA apoenzyme and the covalent RtcA-AMP intermediate, they illuminate the mechanism of nucleotidyl transfer, especially the stereochemical transitions at the AMP phosphate, the critical role of the metal in orienting the PP(i) leaving group of ATP during step 1, and the protein conformational switches that accompany substrate binding and product release. The octahedral metal complex of RtcA•ATP•Mn(2+) includes nonbridging oxygens from each of the ATP phosphates, two waters, and Glu14 as the sole RtcA component. Whereas the RtcA adenylylation step is metal-catalyzed, the subsequent steps in the cyclization pathway are metal-independent.

PubMed: 22167800
DOI: 10.1073/pnas.1115560108

実験手法

X-RAY DIFFRACTION (1.58 Å)