2rnt
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THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE AT 1.8 ANGSTROMS RESOLUTION
OverviewOverview
The enzyme ribonuclease T1 (RNase T1) isolated from Aspergillus oryzae was, cocrystallized with the specific inhibitor guanylyl-2',5'-guanosine, (2',5'-GpG) and the structure refined by the stereochemically restrained, least-squares refinement method to a crystallographic R-factor of 14.9%, for X-ray data above 3 sigma in the resolution range 6 to 1.8 A. The, refined model consists of 781 protein atoms, 43 inhibitor atoms in a major, site and 29 inhibitor atoms in a minor site, 107 water oxygen atoms, and a, metal site assigned as Ca. At the end of the refinement, the orientation, of His, Asn and Gln side-chains was reinterpreted on the basis of, two-dimensional nuclear magnetic resonance data. The crystal packing and, enzyme conformation of the RNase T1/2',5'-GpG complex and of the, near-isomorphous RNase T1/2'-GMP complex are comparable. The, root-mean-square deviation is 0.73 A between equivalent protein atoms., Differences in the unit cell dimensions are mainly due to the bound, inhibitor. The 5'-terminal guanine of 2',5'-GpG binds to RNase T1 in much, the same way as in the 2'-GMP complex. In contrast, the hydrogen bonds, between the catalytic center and the phosphate group are different and the, 3'-terminal guanine forms no hydrogen bonds with the enzyme. This poor, binding is reflected in a 2-fold disorder of 2',5'-GpG (except the, 5'-terminal guanine), which originates from differences in the pucker of, the 5'-terminal ribose. The pucker is C2'-exo for the major site (2/3, occupancy) and C1'-endo for the minor site (1/3 occupancy). The, orientation of the major site is stabilized through stacking interactions, between the 3'-terminal guanine and His92, an amino acid necessary for, catalysis. This might explain the high inhibition rate observed for, 2',5'-GpG, which exceeds that of all other inhibitors of type 2',5'-GpN., On the basis of distance criteria, one solvent peak in the electron, density was identified as metal ion, probably Ca2+. The ion is, co-ordinated by the two Asp15 carboxylate oxygen atoms and by six water, molecules. The co-ordination polyhedron displays approximate 4m2 symmetry.
About this StructureAbout this Structure
2RNT is a Single protein structure of sequence from Aspergillus oryzae with CA and GPG as ligands. Active as Ribonuclease T(1), with EC number 3.1.27.3 Full crystallographic information is available from OCA.
ReferenceReference
Three-dimensional structure of ribonuclease T1 complexed with guanylyl-2',5'-guanosine at 1.8 A resolution., Koepke J, Maslowska M, Heinemann U, Saenger W, J Mol Biol. 1989 Apr 5;206(3):475-88. PMID:2541256
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