1MAS

PURINE NUCLEOSIDE HYDROLASE

Summary for 1MAS

• Entry DOI: 10.2210/pdb1mas/pdb
• Descriptor: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE, POTASSIUM ION (3 entities in total)
• Functional Keywords: hydrolase, purine nucleoside hydrolase, purine nucleosidase, iu-nh
• Biological source: Crithidia fasciculata
• Total number of polymer chains: 2
• Total formula weight: 68491.16

Authors

Degano, M.,Gopaul, D.N.,Scapin, G.,Schramm, V.L.,Sacchettini, J.C. (deposition date: 1995-12-18, release date: 1996-08-17, Last modification date: 2024-02-14)

Primary citation

Degano, M.,Gopaul, D.N.,Scapin, G.,Schramm, V.L.,Sacchettini, J.C.
Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata.
Biochemistry, 35:5971-5981, 1996

PubMed Abstract: Protozoan parasites rely on the host for purines since they lack a de novo synthetic pathway. Crithidia fasciculata salvages exogenous inosine primarily through hydrolysis of the N-ribosidic bond using several nucleoside hydrolases. The most abundant nucleoside hydrolase is relatively nonspecific but prefers inosine and uridine as substrates. Here we report the three-dimensional structure of the inosine-uridine nucleoside hydrolase (IU-NH) from C. fasciculata determined by X-ray crystallography at a nominal resolution of 2.5 A. The enzyme has an open (alpha, beta) structure which differs from the classical dinucleotide binding fold. IU-nucleoside hydrolase is composed of a mixed eight-stranded beta sheet surrounded by six alpha helices and a small C-terminal lobe composed of four alpha helices. Two short antiparallel beta strands are involved in intermolecular contacts. The catalytic pocket is located at the C-terminal end of beta strands beta 1 and beta 4. Four aspartate residues are located at the bottom of the cavity in a geometry which suggests interaction with the ribose moiety of the nucleoside. These groups could provide the catalytically important interactions to the ribosyl hydroxyls and the stabilizing anion for the oxycarbonium-like transition state. Histidine 241, located on the side of the active site cavity, is the proposed proton donor which facilitates purine base departure [Gopaul, D. N., Meyer, S. L., Degano, M., Sacchettini, J. C., & Schramm, V. L. (1996) Biochemistry 35, 5963-5970]. The substrate binding site is unlike that from purine nucleoside phosphorylase, phosphoribosyltransferases, or uracil DNA glycosylase and thus represents a novel architecture for general acid-base catalysis. This detailed knowledge of the architecture of the active site, together with the previous transition state analysis [Horenstein, B. A., Parkin, D. W., Estupiñán, B., & Schramm, V. L. (1991) Biochemistry 30, 10788-10795], allows analysis of the interactions leading to catalysis and an explanation for the tight-binding inhibitors of the enzyme [Schramm, V. L., Horenstein, B. A., & Kline, P. C. (1994) J. Biol. Chem. 269, 18259-18262].

PubMed: 8634238
DOI: 10.1021/bi952999m

Experimental method

X-RAY DIFFRACTION (2.5 Å)