Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: Nuclease-H124L and its ternary complex with Ca^2+ and thymidine-3′,5′-bisphosphate
Authors: Wang, J.; Truckses, D.M.; Abildgaard, F.; Džakula, Z.; Zolnai, Z.; Markley, J.L.
Source: Journal of Biomolecular NMR, Volume 10, Number 2, September 1997 , pp. 143-164(22)
Abstract:The solution structures of staphylococcal nuclease (nuclease) H124L and its ternary complex, (nuclease-H124L)•pdTp•Ca^2+, were determined by ab initio dynamic simulated annealing using 1925 NOE, 119 , 20 ^1 and 112 hydrogen bond constraints for the free protein, and 2003 NOE, 118 , 20 ^1 and 114 hydrogen bond constraints for the ternary complex. In both cases, the final structures display only small deviations from idealized covalent geometry. In structured regions, the overall root-mean-square deviations from mean atomic coordinates are 0.46 (±0.05) Å and 0.41 (±0.05) Å for the backbone heavy atoms of nuclease and its ternary complex, respectively. The backbone conformations of residues in the loop formed by Arg^81–Gly^86, which is adjacent to the active site, are more precisely defined in the ternary complex than in unligated nuclease. Also, the protein side chains that show NOEs and evidence for hydrogen bonds to pdTp (Arg^35, Lys^84, Tyr^85, Arg^87, Tyr^113, and Tyr^115) are better defined in the ternary complex. As has been observed previously in the X-ray structures of nuclease-WT, the binding of pdTp causes the backbone of Tyr^113 to change from an extended to a left-handed α-helical conformation. The NMR structures reported here were compared with available X-ray structures: nuclease-H124L [Truckses et al. (1996) Protein Sci., 5, 1907–1916] and the ternary complex of wild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct. Funct. Genet., 5, 183–201]. Overall, the solution structures of nuclease-H124L are consistent with these crystal structures, but small differences were observed between the structures in the solution and crystal environments. These included differences in the conformations of certain side chains, a reduction in the extent of helix 1 in solution, and many fewer hydrogen bonds involving side chains in solution.
Keywords: Comparison of NMR and X-ray structures; Distance constraints from NOEs; Hydrogen bond constraints; Inhibitor binding; Stereospecific assignments; Structure refinement; Torsion angle constraints from J-coupling
Document Type: Regular Paper
Affiliations: Department of Biochemistry, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, U.S.A.
Publication date: 1997-09-01