1QD2

CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG

1QD2 の概要

• エントリーDOI: 10.2210/pdb1qd2/pdb
• 関連するPDBエントリー: 1TCS
• 分子名称: TRICHOSANTHIN, ADENINE (3 entities in total)
• 機能のキーワード: enzyme-product complex obtained from enzyme-substrate analog complex, hydrolase
• 由来する生物種: Trichosanthes kirilowii
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27301.90

構造登録者

Gu, Y.J.,Xia, Z.X. (登録日: 1999-07-09, 公開日: 2000-04-24, 最終更新日: 2024-02-14)

主引用文献

Gu, Y.J.,Xia, Z.X.
Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase.
Proteins, 39:37-46, 2000

PubMed Abstract: Four substrate analogs-nicotinamide adenine dinucleotide, adenylyl (3', 5') guanosine, guanylyl (3',5') adenosine, and adenosine 2', 5'-diphosphate-have been used to prepare the complexes with trichosanthin (TCS), a type I ribosome-inactivating protein that possesses the activity of N-glycosidase. The crystal structures of the complexes have been determined and refined at high resolution. The refined structures show that the N-glycosidic bonds of all the four substrate analogues are hydrolyzed and a common structure is shared by the four complexes, in which only adenine, the product of the enzymatic reaction, is bound in the active center. The structure is compared with those of native trichosanthin and a previously reported trichosanthin-NADPH complex in which the N-glycosidic bond is uncleaved. The structural comparison shows that the conformation of Tyr70 obviously differs from those in the latter two structures, i.e., the side chain of Tyr70 is rotated along its Cbeta-Cgamma bond by approximately 70 degrees. The water molecule found to be preassociated with the N-glycosidic bond in the TCS-NADPH complex structure and proposed to be the water candidate responsible for hydrolyzing the N-glycosidic bond disappears in the trichosanthin-product complex structure. Based on the comparison of the three structures representing the different stages of the enzymatic reaction, the catalytic mechanism of RNA N-glycosidase has been further elucidated. Proteins 2000;39:37-46.

PubMed: 10737925
DOI: 10.1002/(SICI)1097-0134(20000401)39:1<37::AID-PROT4>3.3.CO;2-7

実験手法

X-RAY DIFFRACTION (1.86 Å)