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T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism.
J Mol Biol. 1999 Sep 24; 292(3):717-30.JM

Abstract

beta-Glucosyltransferase (BGT) is a DNA-modifying enzyme encoded by bacteriophage T4 which catalyses the transfer of glucose (Glc) from uridine diphosphoglucose (UDP-Glc) to 5-hydroxymethylcytosine (5-HMC) in double-stranded DNA. The glucosylation of T4 phage DNA is part of a phage DNA protection system aimed at host nucleases. We previously reported the first three-dimensional structure of BGT determined from crystals grown in ammonium sulphate containing UDP-Glc. In this previous structure, we did not observe electron density for the Glc moiety of UDP-Glc nor for two large surface loop regions (residues 68-76 and 109-122). Here we report two further BGT co-crystal structures, in the presence of UDP product (form I) and donor substrate UDP-Glc (form II), respectively. Form I crystals are grown in ammonium sulphate and the structure has been determined to 1.88 A resolution (R -factor 19.1 %). Form II crystals are grown in polyethyleneglycol 4000 and the structure has been solved to 2.3 A resolution (R -factor 19.8 %). The form I structure is isomorphous to our previous BGT UDP-Glc structure. The form II structure, however, has allowed us to model the two missing surface loop regions and thus provides the first complete structural description of BGT. In this low-salt crystal form, we see no electron density for the Glc moiety from UDP-Glc similar to previous observations. Biochemical data however, shows that BGT can cleave UDP-Glc in the absence of DNA acceptor, which probably accounts for the absence of Glc in our UDP-Glc substrate structures. The complete BGT structure now provides a basis for detailed modelling of a BGT HMC-DNA ternary complex. By using the structural similarity between the catalytic core of glycogen phosphorylase (GP) and BGT, we have modelled the position of the Glc moiety in UDP-Glc. From these two models, we propose a catalytic mechanism for BGT and identify residues involved in both DNA binding and in stabilizing a "flipped-out" 5-HMC nucleotide.

Authors+Show Affiliations

Molecular Structure and Function Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Field, London, WC2A 3PX, UK.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

10497034

Citation

Moréra, S, et al. "T4 Phage Beta-glucosyltransferase: Substrate Binding and Proposed Catalytic Mechanism." Journal of Molecular Biology, vol. 292, no. 3, 1999, pp. 717-30.
Moréra S, Imberty A, Aschke-Sonnenborn U, et al. T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism. J Mol Biol. 1999;292(3):717-30.
Moréra, S., Imberty, A., Aschke-Sonnenborn, U., Rüger, W., & Freemont, P. S. (1999). T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism. Journal of Molecular Biology, 292(3), 717-30.
Moréra S, et al. T4 Phage Beta-glucosyltransferase: Substrate Binding and Proposed Catalytic Mechanism. J Mol Biol. 1999 Sep 24;292(3):717-30. PubMed PMID: 10497034.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism. AU - Moréra,S, AU - Imberty,A, AU - Aschke-Sonnenborn,U, AU - Rüger,W, AU - Freemont,P S, PY - 1999/9/25/pubmed PY - 1999/9/25/medline PY - 1999/9/25/entrez SP - 717 EP - 30 JF - Journal of molecular biology JO - J Mol Biol VL - 292 IS - 3 N2 - beta-Glucosyltransferase (BGT) is a DNA-modifying enzyme encoded by bacteriophage T4 which catalyses the transfer of glucose (Glc) from uridine diphosphoglucose (UDP-Glc) to 5-hydroxymethylcytosine (5-HMC) in double-stranded DNA. The glucosylation of T4 phage DNA is part of a phage DNA protection system aimed at host nucleases. We previously reported the first three-dimensional structure of BGT determined from crystals grown in ammonium sulphate containing UDP-Glc. In this previous structure, we did not observe electron density for the Glc moiety of UDP-Glc nor for two large surface loop regions (residues 68-76 and 109-122). Here we report two further BGT co-crystal structures, in the presence of UDP product (form I) and donor substrate UDP-Glc (form II), respectively. Form I crystals are grown in ammonium sulphate and the structure has been determined to 1.88 A resolution (R -factor 19.1 %). Form II crystals are grown in polyethyleneglycol 4000 and the structure has been solved to 2.3 A resolution (R -factor 19.8 %). The form I structure is isomorphous to our previous BGT UDP-Glc structure. The form II structure, however, has allowed us to model the two missing surface loop regions and thus provides the first complete structural description of BGT. In this low-salt crystal form, we see no electron density for the Glc moiety from UDP-Glc similar to previous observations. Biochemical data however, shows that BGT can cleave UDP-Glc in the absence of DNA acceptor, which probably accounts for the absence of Glc in our UDP-Glc substrate structures. The complete BGT structure now provides a basis for detailed modelling of a BGT HMC-DNA ternary complex. By using the structural similarity between the catalytic core of glycogen phosphorylase (GP) and BGT, we have modelled the position of the Glc moiety in UDP-Glc. From these two models, we propose a catalytic mechanism for BGT and identify residues involved in both DNA binding and in stabilizing a "flipped-out" 5-HMC nucleotide. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/10497034/T4_phage_beta_glucosyltransferase:_substrate_binding_and_proposed_catalytic_mechanism_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-2836(99)93094-2 DB - PRIME DP - Unbound Medicine ER -