1RL0

Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30

1RL0 の概要

• エントリーDOI: 10.2210/pdb1rl0/pdb
• 分子名称: Antiviral protein DAP-30 (2 entities in total)
• 機能のキーワード: mixed beta-sheet, alpha and beta regions, hydrolase, plant protein
• 由来する生物種: Dianthus caryophyllus (clove pink)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 28632.63

構造登録者

Fermani, S.,Falini, G.,Ripamonti, A.,Bolognesi, A.,Polito, L.,Stirpe, F. (登録日: 2003-11-24, 公開日: 2004-12-07, 最終更新日: 2023-08-23)

主引用文献

Fermani, S.,Falini, G.,Ripamonti, A.,Polito, L.,Stirpe, F.,Bolognesi, A.
The 1.4A structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins
J.Struct.Biol., 149:204-212, 2005

PubMed Abstract: Ribosome inactivating proteins (RIPs) are plant proteins with enzymatic activity identified as rRNA N-glycosidase (EC 3.2.2.22), which cleaves the N-glycosidic bond of a specific adenine on the ricin/sarcin region of rRNA, thus causing inhibition of protein synthesis. They also depurinate extensively DNA and other polynucleotides. The three-dimensional structure of dianthin 30, a type 1 (single-chain) RIP of Dianthus caryophyllus (leaves), is now described at 1.4 angstroms, a resolution never achieved before for any RIP. The fold typical of RIPs is conserved, despite some differences in the loop regions. The general structure comparison by superimposed alpha-carbon (249 atoms) and the sequence alignment by structure for dianthin 30 and saporin-S6 give a root mean square deviation of 0.625 angstroms. Despite the differences reported for the biological activities of the two RIPs, their structures fit quite well and both show a protein segment containing strands beta7, beta8, and beta9 shorter than other RIPs. However, the surface electrostatic potential in the active site region neatly distinguishes dianthin 30 from saporin-S6. The possible relationship between the charge distribution and the behavior of the proteins toward different substrates is discussed.

PubMed: 15681236
DOI: 10.1016/j.jsb.2004.11.007

実験手法

X-RAY DIFFRACTION (1.4 Å)