ISSN:
1573-5001
Keywords:
Comparison of NMR and X-ray structures
;
Inhibitor binding
;
Stereospecific assignments
;
Distance constraints from NOEs
;
Torsion angle constraints from J-coupling
;
Hydrogen bond constraints
;
Structure refinement
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Chemistry and Pharmacology
Notes:
Abstract The solution structures of staphylococcal nuclease (nuclease) H124L and itsternary complex, (nuclease-H124L)•pdTp•Ca2+, were determinedby ab initio dynamic simulated annealing using 1925 NOE, 119 φ, 20χ1 and 112 hydrogen bond constraints for the free protein,and 2003 NOE, 118 φ, 20 χ1 and 114 hydrogen bondconstraints for the ternary complex. In both cases, the final structuresdisplay only small deviations from idealized covalent geometry. In structuredregions, the overall root-mean-square deviations from mean atomic coordinatesare 0.46 (±0.05) Å and 0.41 (±0.05) Å for thebackbone heavy atoms of nuclease and its ternary complex, respectively. Thebackbone conformations of residues in the loop formed byArg81–Gly86, which is adjacent to the activesite, are more precisely defined in the ternary complex than in unligatednuclease. Also, the protein side chains that show NOEs and evidence forhydrogen bonds to pdTp (Arg35, Lys84,Tyr85, Arg87, Tyr113, andTyr115) are better defined in the ternary complex. As has beenobserved previously in the X-ray structures of nuclease-WT, the binding ofpdTp causes the backbone of Tyr113 to change from an extendedto a left-handed α-helical conformation. The NMR structures reportedhere were compared with available X-ray structures: nuclease-H124L [Truckseset al. (1996) Protein Sci., 5, 1907–1916] and the ternary complex ofwild-type staphylococcal nuclease [Loll and Lattman (1989) Proteins Struct.Funct. Genet., 5, 183–201]. Overall, the solution structures ofnuclease-H124L are consistent with these crystal structures, but smalldifferences were observed between the structures in the solution and crystalenvironments. These included differences in the conformations of certain sidechains, a reduction in the extent of helix 1 in solution, and many fewerhydrogen bonds involving side chains in solution.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1023/A:1018350004729
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