Molecular dynamics simulations of glycosyltransferase LgtC.
Molecular dynamics simulations have been performed on fully solvated alpha-(1-->4)-galactosyltransferase LgtC from Neisseria meningitidis with and without the donor substrate UDP-Gal and in the presence of the manganese ion. The analysis of the trajectories revealed a limited movement in the loop X (residues 75-80) and a larger conformational change in the loop Y (residues 246-251) in the simulation, when UDP-Gal was not present. In this case, the loops X and Y open by almost 10A, exposing the active site to the solvent. The 'hinge region' responsible for the opening is composed of residues 246-247. We have also analyzed the behavior of the manganese ion in the simulations. The coordination number is 6 when UDP-Gal is present and it increases to 7 when it is absent. In the latter case, three water molecules become coordinated to the ion. In both cases, the coordination is very stable implying that the manganese ion is tightly bound in the active site of the enzyme even if UDP-Gal is not present. Further analysis of the structural water molecules location confirmed that the mobility of water molecules in the active site and the accessibility of this site for solvent are higher in the absence of the substrate.
Snajdrová
Lenka
L
Centre de Recherches sur les Macromolécules Végétales, CNRS and Université Joseph Fourier, IFR 2607, BP 53, F-38041 Grenoble, France.
Kulhánek
Petr
P
Imberty
Anne
A
Koca
Jaroslav
J
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D016695:Glycosyltransferases / Q000737:chemistry*; D006639:Histidine / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D007785:Lactose / Q000378:metabolism; D008345:Manganese / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011392:Proline / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D014531:Uridine Diphosphate Galactose / Q000378:metabolism
D001426:Bacterial Proteins; D014531:Uridine Diphosphate Galactose; D008345:Manganese; D006639:Histidine; D011392:Proline; D016695:Glycosyltransferases; C101829:LgtC protein, Neisseria; D007785:Lactose