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. 1986 Jan;49(1):209–219. doi: 10.1016/S0006-3495(86)83635-9

Structure of the crystalline complex between ribonuclease A and D(pA)4.

A McPherson, G Brayer, R Morrison
PMCID: PMC1329623  PMID: 3955171

Abstract

Crystals of a complex formed between ribonuclease A and d(pA)4 were grown and their structure determined by a combination of multiple isomorphous replacement (MIR) and molecular replacement techniques. The known structure of ribonuclease A in the correct orientation in the unit cell yielded a conventional crystallographic R factor of 0.32 at 2.8 A resolution when refined as a rigid body. Difference Fourier syntheses permitted determination of the disposition of the DNA in the unit cell. Refinement of both protein and DNA by constrained-restrained least squares procedures resulted in an R factor of 0.22 at 2.5 A resolution. The structure of the crystalline complex is comprised of four ordered oligomers of d(pA)4 associated with each molecule of RNAse. If the sites of interaction between protein and d(pA)4 fragments are mapped on the surface of the protein, they describe an essentially continuous path into and through the active site, across the surface of the enzyme and finally into the basic amino acid cluster on the opposite side of the protein.

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210FIGURE 1
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210FIGURE 2
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211FIGURE 3
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212FIGURE 6
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Selected References

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

  1. Borkakoti N. Enzyme specificity: base recognition and hydrolysis of RNA by ribonuclease A. FEBS Lett. 1983 Oct 17;162(2):367–373. doi: 10.1016/0014-5793(83)80789-3. [DOI] [PubMed] [Google Scholar]
  2. Borkakoti N., Palmer R. A., Haneef I., Moss D. S. Specificity of pancreatic ribonuclease-A. An X-ray study of a protein-nucleotide complex. J Mol Biol. 1983 Sep 25;169(3):743–755. doi: 10.1016/s0022-2836(83)80168-5. [DOI] [PubMed] [Google Scholar]
  3. Brayer G. D., McPherson A. Mechanism of DNA binding to the gene 5 protein of bacteriophage fd. Biochemistry. 1984 Jan 17;23(2):340–349. doi: 10.1021/bi00297a025. [DOI] [PubMed] [Google Scholar]
  4. Brayer G. D., McPherson A. Preliminary diffraction data for crystals of ribonucleases A and B and their complexes with deoxy(pA)4 and deoxy(pA)6. J Biol Chem. 1982 Apr 10;257(7):3359–3361. [PubMed] [Google Scholar]
  5. Carlisle C. H., Palmer R. A., Mazumdar S. K., Gorinsky B. A., Yeates D. G. The structure of ribonuclease at 2-5 Angström resolution. J Mol Biol. 1974 May 5;85(1):1–18. doi: 10.1016/0022-2836(74)90125-9. [DOI] [PubMed] [Google Scholar]
  6. FELSENFELD G., SANDEEN G., VONHIPPEL P. H. THE DESTABILIZING EFFECT OF RIBONUCLEASE ON THE HELICAL DNA STRUCTURE. Proc Natl Acad Sci U S A. 1963 Oct;50:644–651. doi: 10.1073/pnas.50.4.644. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Jensen D. E., von Hippel P. H. DNA "melting" proteins. I. Effects of bovine pancreatic ribonuclease binding on the conformation and stability of DNA. J Biol Chem. 1976 Nov 25;251(22):7198–7214. [PubMed] [Google Scholar]
  8. Karpel R. L., Yrttimaa V. A., Patel G. L. A helix-destabilizing protein substrate devoid of heterocyclic bases. Biochem Biophys Res Commun. 1981 May 29;100(2):760–768. doi: 10.1016/s0006-291x(81)80240-9. [DOI] [PubMed] [Google Scholar]
  9. Kartha G., Bello J., Harker D. Tertiary structure of ribonuclease. Nature. 1967 Mar 4;213(5079):862–865. doi: 10.1038/213862a0. [DOI] [PubMed] [Google Scholar]
  10. Matthew J. B., Richards F. M. Anion binding and pH-dependent electrostatic effects in ribonuclease. Biochemistry. 1982 Sep 28;21(20):4989–4999. doi: 10.1021/bi00263a024. [DOI] [PubMed] [Google Scholar]
  11. McPherson A., Wang A. H., Jurnak F. A., Molineux I., Kolpak F., Rich A. X-ray diffraction studies on crystalline complexes of the gene 5 DNA-unwinding protein with deoxyoligonucleotides. J Biol Chem. 1980 Apr 10;255(7):3174–3177. [PubMed] [Google Scholar]
  12. Pavlovsky A. G., Borisova S. N., Borisov V. V., Antonov I. V., Karpeisky M. Y. The structure of the complex of ribonuclease S with fluoride analogue of UpA at 2.5 A resolution. FEBS Lett. 1978 Aug 15;92(2):258–262. doi: 10.1016/0014-5793(78)80766-2. [DOI] [PubMed] [Google Scholar]
  13. Record M. T., Jr, Lohman M. L., De Haseth P. Ion effects on ligand-nucleic acid interactions. J Mol Biol. 1976 Oct 25;107(2):145–158. doi: 10.1016/s0022-2836(76)80023-x. [DOI] [PubMed] [Google Scholar]
  14. Wlodawer A., Miller M., Sjölin L. Active site of RNase: neutron diffraction study of a complex with uridine vanadate, a transition-state analog. Proc Natl Acad Sci U S A. 1983 Jun;80(12):3628–3631. doi: 10.1073/pnas.80.12.3628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Wlodawer A., Sjölin L. Structure of ribonuclease A: results of joint neutron and X-ray refinement at 2.0-A resolution. Biochemistry. 1983 May 24;22(11):2720–2728. doi: 10.1021/bi00280a021. [DOI] [PubMed] [Google Scholar]
  16. Wodak S. Y. The structure of cytidilyl(2',5')adenosine when bound to pancreatic ribonuclease S. J Mol Biol. 1977 Nov;116(4):855–875. doi: 10.1016/0022-2836(77)90275-3. [DOI] [PubMed] [Google Scholar]
  17. Wyckoff H. W., Tsernoglou D., Hanson A. W., Knox J. R., Lee B., Richards F. M. The three-dimensional structure of ribonuclease-S. Interpretation of an electron density map at a nominal resolution of 2 A. J Biol Chem. 1970 Jan 25;245(2):305–328. [PubMed] [Google Scholar]

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