1f8x

CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASECRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE

Structural highlights 1f8x is a 2 chain structure with sequence from Lactobacillus leichmannii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Activity: Nucleoside deoxyribosyltransferase, with EC number 2.4.2.6 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [NTD_LACLE] Catalyzes the cleavage of the glycosidic bond of 2'-deoxyribonucleosides and the transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed BACKGROUND: Nucleoside 2-deoxyribosyltransferase plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. The kinetics describe a ping-pong-bi-bi pathway involving the formation of a covalent enzyme-deoxyribose intermediate. The enzyme is produced by a limited number of microorganisms and its functions have been exploited in its use as a biocatalyst to synthesize nucleoside analogs of therapeutic interest. RESULTS: We describe the crystal structure of the enzyme with and without bound ligand. The native structure was solved by the single isomorphous replacement with anomalous scattering method (SIRAS) and refined to 2.5 A resolution resulting in a crystallographic R factor of 16.6%. The enzyme comprises a single domain that belongs to the general class of doubly-wound alpha/beta proteins; it also exhibits a unique nucleoside-binding motif. X-ray analysis of enzyme-purine and enzyme-pyrimidine complexes presented here reveals that the active site lies in a cleft formed by the edge of the beta sheet and two alpha helices and contains side chains from two subunits. CONCLUSIONS: These results indicate residues that may be important in substrate binding and catalysis and thus may serve as a framework for elucidating the mechanism of enzyme activity. In particular, the proposed nucleophile, Glu98, lies in the nucleoside-binding pocket at an appropriate position for nucleophilic attack. A comparison of the enzyme interactions with both a purine and pyrimidine ligand provides some insight into the structural basis for enzyme specificity. Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.,Armstrong SR, Cook WJ, Short SA, Ealick SE Structure. 1996 Jan 15;4(1):97-107. PMID:8805514 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

spinqualitylabelsall models 1f8x, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image