1B8O

PURINE NUCLEOSIDE PHOSPHORYLASE

1B8O の概要

• エントリーDOI: 10.2210/pdb1b8o/pdb
• 分子名称: PURINE NUCLEOSIDE PHOSPHORYLASE, MAGNESIUM ION, PHOSPHATE ION, ... (5 entities in total)
• 機能のキーワード: pentosyltransferase, purine nucleoside phosphorylase, transferase
• 由来する生物種: Bos taurus (cattle)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 32072.64

構造登録者

Fedorov, A.A.,Kicska, G.A.,Fedorov, E.V.,Shi, W.,Tyler, P.C.,Furneaux, R.H.,Schramm, V.L.,Almo, S.C. (登録日: 1999-02-02, 公開日: 1999-02-08, 最終更新日: 2023-09-20)

主引用文献

Fedorov, A.,Shi, W.,Kicska, G.,Fedorov, E.,Tyler, P.C.,Furneaux, R.H.,Hanson, J.C.,Gainsford, G.J.,Larese, J.Z.,Schramm, V.L.,Almo, S.C.
Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis.
Biochemistry, 40:853-860, 2001

PubMed Abstract: Immucillin-H [ImmH; (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol] is a 23 pM inhibitor of bovine purine nucleoside phosphorylase (PNP) specifically designed as a transition state mimic [Miles, R. W., Tyler, P. C., Furneaux, R. H., Bagdassarian, C. K., and Schramm, V. L. (1998) Biochemistry 37, 8615-8621]. Cocrystals of PNP and the inhibitor are used to provide structural information for each step through the reaction coordinate of PNP. The X-ray crystal structure of free ImmH was solved at 0.9 A resolution, and a complex of PNP.ImmH.PO(4) was solved at 1.5 A resolution. These structures are compared to previously reported complexes of PNP with substrate and product analogues in the catalytic sites and with the experimentally determined transition state structure. Upon binding, ImmH is distorted to a conformation favoring ribosyl oxocarbenium ion formation. Ribosyl destabilization and transition state stabilization of the ribosyl oxocarbenium ion occur from neighboring group interactions with the phosphate anion and the 5'-hydroxyl of the ribosyl group. Leaving group activation of hypoxanthine involves hydrogen bonds to O6, N1, and N7 of the purine ring. Ordered water molecules provide a proton transfer bridge to O6 and N7 and permit reversible formation of these hydrogen bonds. Contacts between PNP and catalytic site ligands are shorter in the transition state analogue complex of PNP.ImmH.PO(4) than in the Michaelis complexes of PNP.inosine.SO(4) or PNP.hypoxanthine.ribose 1-PO(4). Reaction coordinate motion is dominated by translation of the carbon 1' of ribose between relatively fixed phosphate and purine groups. Purine and pyrimidine phosphoribosyltransferases and nucleoside N-ribosyl hydrolases appear to operate by a similar mechanism.

PubMed: 11170405
DOI: 10.1021/bi002499f

実験手法

X-RAY DIFFRACTION (1.5 Å)