2VUG

The structure of an archaeal homodimeric RNA ligase

2VUG の概要

• エントリーDOI: 10.2210/pdb2vug/pdb
• 分子名称: PAB1020, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• 機能のキーワード: rna, ligase, amppnp, pab1020, pyrococcus abyssi, nucleotidyl- transferase
• 由来する生物種: PYROCOCCUS ABYSSI GE5 (PYROCOCCUS ABYSSI STR. ORSAY)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 92696.49

構造登録者

Brooks, M.A.,Meslet-Cladiere, L.,Graille, M.,Kuhn, J.,Blondeau, K.,Myllykallio, H.,van Tilbeurgh, H. (登録日: 2008-05-26, 公開日: 2008-06-03, 最終更新日: 2024-05-08)

主引用文献

Brooks, M.A.,Meslet-Cladiere, L.,Graille, M.,Kuhn, J.,Blondeau, K.,Myllykallio, H.,van Tilbeurgh, H.
The structure of an archaeal homodimeric ligase which has RNA circularization activity.
Protein Sci., 17:1336-1345, 2008

PubMed Abstract: The genome of Pyrococcus abyssi contains two open reading frames encoding proteins which had been previously predicted to be DNA ligases, Pab2002 and Pab1020. We show that while the former is indeed a DNA ligase, Pab1020 had no effect on the substrate deoxyoligo-ribonucleotides tested. Instead, Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction, suggesting that it is an RNA ligase. We have solved the structure of Pab1020 in complex with the ATP analog AMPPNP by single-wavelength anomalous dispersion (SAD), elucidating a structure with high structural similarity to the catalytic domains of two RNA ligases from the bacteriophage T4. Additional carboxy-terminal domains are also present, and one of these mediates contacts with a second protomer, which is related by noncrystallographic symmetry, generating a homodimeric structure. These C-terminal domains are terminated by short domain swaps which themselves end within 5 A of the active sites of the partner molecules. Additionally, we show that the protein is indeed capable of circularizing RNA molecules in an ATP-dependent reaction. These structural and biochemical results provide an insight into the potential physiological roles of Pab1020.

PubMed: 18511537
DOI: 10.1110/ps.035493.108

実験手法

X-RAY DIFFRACTION (2.9 Å)