1RPG

STRUCTURES OF RNASE A COMPLEXED WITH 3'-CMP AND D(CPA): ACTIVE SITE CONFORMATION AND CONSERVED WATER MOLECULES

1RPG の概要

• エントリーDOI: 10.2210/pdb1rpg/pdb
• 分子名称: RIBONUCLEASE A, 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• 機能のキーワード: hydrolase(phosphoric diester)
• 由来する生物種: Bos taurus (cattle)
• 細胞内の位置: Secreted: P61823
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 14366.92

構造登録者

Zegers, I.,Wyns, L.,Palmer, R. (登録日: 1994-08-29, 公開日: 1994-12-20, 最終更新日: 2024-11-13)

主引用文献

Zegers, I.,Maes, D.,Dao-Thi, M.H.,Poortmans, F.,Palmer, R.,Wyns, L.
The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.
Protein Sci., 3:2322-2339, 1994

PubMed Abstract: The interactions of RNase A with cytidine 3'-monophosphate (3'-CMP) and deoxycytidyl-3',5'-deoxyadenosine (d(CpA)) were analyzed by X-ray crystallography. The 3'-CMP complex and the native structure were determined from trigonal crystals, and the d(CpA) complex from monoclinic crystals. The differences between the overall structures are concentrated in loop regions and are relatively small. The protein-inhibitor contacts are interpreted in terms of the catalytic mechanism. The general base His 12 interacts with the 2' oxygen, as does the electrostatic catalyst Lys 41. The general acid His 119 has 2 conformations (A and B) in the native structure and is found in, respectively, the A and the B conformation in the d(CpA) and the 3'-CMP complex. From the present structures and from a comparison with RNase T1, we propose that His 119 is active in the A conformation. The structure of the d(CpA) complex permits a detailed analysis of the downstream binding site, which includes His 119 and Asn 71. The comparison of the present RNase A structures with an inhibitor complex of RNase T1 shows that there are important similarities in the active sites of these 2 enzymes, despite the absence of any sequence homology. The water molecules were analyzed in order to identify conserved water sites. Seventeen water sites were found to be conserved in RNase A structures from 5 different space groups. It is proposed that 7 of those water molecules play a role in the binding of the N-terminal helix to the rest of the protein and in the stabilization of the active site.

PubMed: 7756988

実験手法

X-RAY DIFFRACTION (1.4 Å)