3RTJ

Crystal structure of ricin bound with dinucleotide ApG

「1APG」から置き換えられました

3RTJ の概要

• エントリーDOI: 10.2210/pdb3rtj/pdb
• 関連するPDBエントリー: 2AAI 3RTI
• 関連するBIRD辞書のPRD_ID: PRD_900004
• 分子名称: RNA (5'-R(*AP*G)-3'), Ricin A chain, Ricin B chain, ... (5 entities in total)
• 機能のキーワード: enzyme-substrate complex, glycosidase ribosome-inactivating protein lectin glycoprotein, lactose binding, glycosylation, hydrolase, hydrolase-rna complex, hydrolase/rna
• 由来する生物種: Ricinus communis (Castor bean); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 61089.19

構造登録者

Monzingo, A.F.,Robertus, J.D. (登録日: 2011-05-03, 公開日: 2011-08-31, 最終更新日: 2024-10-30)

主引用文献

Monzingo, A.F.,Robertus, J.D.
X-ray analysis of substrate analogs in the ricin A-chain active site.
J.Mol.Biol., 227:1136-1145, 1992

PubMed Abstract: Ricin A-chain is an N-glycosidase that hydrolyzes the adenine ring from a specific adenosine of rRNA. Formycin monophosphate (FMP) and adenyl(3'-->5')guanosine (ApG) were bound to ricin A-chain and their structures elucidated by X-ray crystallography. The formycin ring stacks between tyrosines 80 and 123 and at least four hydrogen bonds are made to the adenine moiety. A residue invariant in this enzyme class, Arg180, appears to hydrogen bond to N-3 of the susceptible adenine. Three hypothetical models for binding a true hexanucleotide substrate, CGAGAG, are proposed. They incorporate adenine binding, shown by crystallography, but also include geometry likely to favor catalysis. For example, efforts have been made to orient the ribose ring in a way that allows solvent attack and oxycarbonium stabilization by the enzyme. The favored model is a simple perturbation of the tetraloop structure determined by nuclear magnetic resonance for similar polynucleotides. The model is attractive in that specific roles are defined for conserved protein residues. A mechanism of action is proposed. It invokes oxycarbonium ion stabilization on ribose by Glu177 in the transition state. Arg180 stabilizes anion development on the leaving adenine by protonation at N-3 and may activate a trapped water molecule that is the ultimate nucleophile in the depurination.

PubMed: 1433290

実験手法

X-RAY DIFFRACTION (3 Å)