Crystal structure of the DNA modifying enzyme beta‐glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose

• Published in: The EMBO journal Vol. 13; no. 15; pp. 3413 - 3422
• Main Authors: Vrielink, A., Rüger, W., Driessen, H.P., Freemont, P.S.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group 01-08-1994
• Subjects: Analytical, structural and metabolic biochemistry; Bacteriophage T4 - enzymology; Binding Sites; Biological and medical sciences; Catalysis; Computer Graphics; Crystalline structure; Crystallization; Crystallography, X-Ray; DNA - metabolism; Enzymes and enzyme inhibitors; Fundamental and applied biological sciences. Psychology; Glucose - metabolism; Glucosyltransferases - chemistry; Glucosyltransferases - metabolism; Models, Molecular; Molecular biophysics; Molecular Structure; phage T4; Protein Conformation; Structure in molecular biology; Transferases; Uridine Diphosphate Glucose - chemistry; Uridine Diphosphate Glucose - metabolism; Ligand binding; Enzyme; Transferases; Glycosyltransferases; Refinement; Binding site; Glucose; Substrate enzyme complex; DNA β-glucosyltransferase; Myoviridae; Virus; T even phage; DNA; Molecular model; Hexosyltransferases; Phage; Structural analysis; Phage T4; Ose nucleotide; Crystalline structure; Conformational transition
• ISSN: 0261-4189; 1460-2075
• DOI: 10.1002/j.1460-2075.1994.tb06646.x

Bacteriophage T4 beta‐glucosyltransferase (EC 2.4.1.27) catalyses the transfer of glucose from uridine diphosphoglucose to hydroxymethyl groups of modified cytosine bases in T4 duplex DNA forming beta‐glycosidic linkages. The enzyme forms part of a phage DNA protection system. We have solved and refined the crystal structure of recombinant beta‐glucosyltransferase to 2.2 A resolution in the presence and absence of the substrate, uridine diphosphoglucose. The structure comprises two domains of similar topology, each reminiscent of a nucleotide binding fold. The two domains are separated by a central cleft which generates a concave surface along one side of the molecule. The substrate‐bound complex reveals only clear electron density for the uridine diphosphate portion of the substrate. The UDPG is bound in a pocket at the bottom of the cleft between the two domains and makes extensive hydrogen bonding contacts with residues of the C‐terminal domain only. The domains undergo a rigid body conformational change causing the structure to adopt a more closed conformation upon ligand binding. The movement of the domains is facilitated by a hinge region between residues 166 and 172. Electrostatic surface potential calculations reveal a large positive potential along the concave surface of the structure, suggesting a possible site for duplex DNA interaction.