title: Crystal structure of RNase T1 complexed with the product nucleotide 3'-GMP. Structural evidence for direct interaction of histidine 40 and glutamic acid 58 with the 2'-hydroxyl group of the ribose.
abstract: The crystal structure of RNase T1 complexed with 3'-GMP has been determined. The glycosyl conformation of 3'-GMP is in the syn conformation, and the ribose adopts the O4'-endo pucker. This observed pucker is different from that in any complex structures of RNase T1. In the present complex, this energetically unfavorable conformation is stabilized by the water molecule with the bridged hydrogen bonds between the O2' and the O3' atoms of the ribose. The guanine base is recognized in the same manner as observed in the complex of 2'-GMP. The 2'-hydroxyl group of the ribose shows a tight hydrogen bond to both His-40 and Glu-58 with the suitable geometry for the proton transfer. These hydrogen bonds suggest that the two residues can participate directly in the proton transfer. His-92 is hydrogen bonded to two the proton transfer. His-92 is hydrogen bonded to two oxygen atoms of the phosphate group. Based on the geometry in the active site, the O1P atom may correspond to the O5' atom of the leaving nucleotide in the phosphoryl transfer or a water molecule as a nucleophile in the hydrolysis reaction. In the present complex, the conformations of the 3'-GMP molecule and the side chains of the catalytic residues would be represented as the conformation before the phosphoryl transfer reaction and/or after the hydrolysis reaction.
authors.affiliation: Faculty of Pharmaceutical Sciences, Osaka University, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Gohda
authors.forename: K
authors.initials: K
authors.lastname: Oka
authors.forename: K
authors.initials: K
authors.lastname: Tomita
authors.forename: T
authors.initials: T
authors.lastname: Hakoshima
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D005971:Glutamates / Q000737:chemistry; D018698:Glutamic Acid; D006157:Guanosine Monophosphate / Q000737:chemistry*; D006639:Histidine / Q000737:chemistry; D006860:Hydrogen Bonding; D017665:Hydroxyl Radical / Q000737:chemistry; D007536:Isomerism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D006163:Ribonuclease T1 / Q000737:chemistry*
chemical_list: D005971:Glutamates; D017665:Hydroxyl Radical; D018698:Glutamic Acid; D006639:Histidine; C068152:3'-guanylic acid; D006157:Guanosine Monophosphate; D006163:Ribonuclease T1