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. 1993 Apr 15;90(8):3275–3279. doi: 10.1073/pnas.90.8.3275

The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease.

L J Keefe 1, J Sondek 1, D Shortle 1, E E Lattman 1
PMCID: PMC46282  PMID: 8475069

Abstract

The x-ray crystal structure of a mutant of staphylococcal nuclease that contains a single glycine residue inserted in the C-terminal alpha-helix has been solved to 1.67 A resolution and refined to a crystallographic R value of 0.170. This inserted glycine residue is accommodated in the alpha-helix by formation of a previously uncharacterized bulge, which we term the alpha aneurism. A conformational search of known protein structures has identified the alpha aneurism in a number of protein families, including the histocompatibility antigens and hemoglobins.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arnone A., Bier C. J., Cotton F. A., Day V. W., Hazen E. E., Jr, Richardson D. C., Yonath A., Richardson J. S. A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing. J Biol Chem. 1971 Apr 10;246(7):2302–2316. [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. doi: 10.1126/science.235.4787.458. [DOI] [PubMed] [Google Scholar]
  4. Eriksson A. E., Baase W. A., Zhang X. J., Heinz D. W., Blaber M., Baldwin E. P., Matthews B. W. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 1992 Jan 10;255(5041):178–183. doi: 10.1126/science.1553543. [DOI] [PubMed] [Google Scholar]
  5. Garrett T. P., Saper M. A., Bjorkman P. J., Strominger J. L., Wiley D. C. Specificity pockets for the side chains of peptide antigens in HLA-Aw68. Nature. 1989 Dec 7;342(6250):692–696. doi: 10.1038/342692a0. [DOI] [PubMed] [Google Scholar]
  6. Loll P. J., Lattman E. E. The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A. Proteins. 1989;5(3):183–201. doi: 10.1002/prot.340050302. [DOI] [PubMed] [Google Scholar]
  7. Presta L. G., Rose G. D. Helix signals in proteins. Science. 1988 Jun 17;240(4859):1632–1641. doi: 10.1126/science.2837824. [DOI] [PubMed] [Google Scholar]
  8. Sondek J., Shortle D. A general strategy for random insertion and substitution mutagenesis: substoichiometric coupling of trinucleotide phosphoramidites. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3581–3585. doi: 10.1073/pnas.89.8.3581. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Sondek J., Shortle D. Accommodation of single amino acid insertions by the native state of staphylococcal nuclease. Proteins. 1990;7(4):299–305. doi: 10.1002/prot.340070402. [DOI] [PubMed] [Google Scholar]
  10. Sondek J., Shortle D. Structural and energetic differences between insertions and substitutions in staphylococcal nuclease. Proteins. 1992 Apr;13(2):132–140. doi: 10.1002/prot.340130206. [DOI] [PubMed] [Google Scholar]
  11. Stallings W. C., Pattridge K. A., Strong R. K., Ludwig M. L. The structure of manganese superoxide dismutase from Thermus thermophilus HB8 at 2.4-A resolution. J Biol Chem. 1985 Dec 25;260(30):16424–16432. [PubMed] [Google Scholar]
  12. Tucker P. W., Hazen E. E., Jr, Cotton F. A. Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. I. Isolation; physical and enzymatic properties. Mol Cell Biochem. 1978 Dec 22;22(2-3):67–77. doi: 10.1007/BF00496235. [DOI] [PubMed] [Google Scholar]
  13. Tucker P. W., Hazen E. E., Jr, Cotton F. A. Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. II. Solution studies of the nucleotide binding site and the effects of nucleotide binding. Mol Cell Biochem. 1979 Jan 15;23(1):3–16. doi: 10.1007/BF00226675. [DOI] [PubMed] [Google Scholar]
  14. Tucker P. W., Hazen E. E., Jr, Cotton F. A. Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. III. Correlation of the three-dimensional structure with the mechanisms of enzymatic action. Mol Cell Biochem. 1979 Jan 26;23(2):67–86. doi: 10.1007/BF00226229. [DOI] [PubMed] [Google Scholar]
  15. Tucker P. W., Hazen E. E., Jr, Cotton F. A. Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. IV. The nuclease as a model for protein folding. Mol Cell Biochem. 1979 Feb 9;23(3):131–141. doi: 10.1007/BF00219452. [DOI] [PubMed] [Google Scholar]

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