Skip to main content
NCBI home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1994 Dec;3(12):2455–2458. doi: 10.1002/pro.5560031231

The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences.

N V Grishin 1, M A Phillips 1
PMCID: PMC2142754  PMID: 7757001

Abstract

It is well established that, within families of homologous enzymes, amino acid residues that are involved in the chemistry of the reaction are highly conserved. To determine if residues at the subunit interface of oligomeric enzymes with shared active sites are also conserved, comparative analysis of five enzyme families was undertaken. For the chosen enzyme families, sequence data were available for a large number of proteins and a three-dimensional structure was known for at least two members of each family. The analysis indicates that the subunit interface and the hydrophobic core of proteins from all five families have diverged to a similar extent to the overall protein sequences.

Full Text

The Full Text of this article is available as a PDF (386.1 KB).

Selected References

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

  1. Babé L. M., Pichuantes S., Craik C. S. Inhibition of HIV protease activity by heterodimer formation. Biochemistry. 1991 Jan 8;30(1):106–111. doi: 10.1021/bi00215a016. [DOI] [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. Chothia C., Lesk A. M. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986 Apr;5(4):823–826. doi: 10.1002/j.1460-2075.1986.tb04288.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Finer-Moore J. S., Montfort W. R., Stroud R. M. Pairwise specificity and sequential binding in enzyme catalysis: thymidylate synthase. Biochemistry. 1990 Jul 31;29(30):6977–6986. doi: 10.1021/bi00482a005. [DOI] [PubMed] [Google Scholar]
  5. Gouaux J. E., Lipscomb W. N. Three-dimensional structure of carbamoyl phosphate and succinate bound to aspartate carbamoyltransferase. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4205–4208. doi: 10.1073/pnas.85.12.4205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Honzatko R. B., Crawford J. L., Monaco H. L., Ladner J. E., Ewards B. F., Evans D. R., Warren S. G., Wiley D. C., Ladner R. C., Lipscomb W. N. Crystal and molecular structures of native and CTP-liganded aspartate carbamoyltransferase from Escherichia coli. J Mol Biol. 1982 Sep 15;160(2):219–263. doi: 10.1016/0022-2836(82)90175-9. [DOI] [PubMed] [Google Scholar]
  7. Kamitori S., Hirotsu K., Higuchi T., Kondo K., Inoue K., Kuramitsu S., Kagamiyama H., Higuchi Y., Yasuoka N., Kusunoki M. Three-dimensional structure of aspartate aminotransferase from Escherichia coli at 2.8 A resolution. J Biochem. 1988 Sep;104(3):317–318. doi: 10.1093/oxfordjournals.jbchem.a122464. [DOI] [PubMed] [Google Scholar]
  8. Karplus P. A., Schulz G. E. Refined structure of glutathione reductase at 1.54 A resolution. J Mol Biol. 1987 Jun 5;195(3):701–729. doi: 10.1016/0022-2836(87)90191-4. [DOI] [PubMed] [Google Scholar]
  9. Ke H. M., Honzatko R. B., Lipscomb W. N. Structure of unligated aspartate carbamoyltransferase of Escherichia coli at 2.6-A resolution. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4037–4040. doi: 10.1073/pnas.81.13.4037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ke H. M., Lipscomb W. N., Cho Y. J., Honzatko R. B. Complex of N-phosphonacetyl-L-aspartate with aspartate carbamoyltransferase. X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms. J Mol Biol. 1988 Dec 5;204(3):725–747. doi: 10.1016/0022-2836(88)90365-8. [DOI] [PubMed] [Google Scholar]
  11. Kim K. H., Pan Z. X., Honzatko R. B., Ke H. M., Lipscomb W. N. Structural asymmetry in the CTP-liganded form of aspartate carbamoyltransferase from Escherichia coli. J Mol Biol. 1987 Aug 20;196(4):853–875. doi: 10.1016/0022-2836(87)90410-4. [DOI] [PubMed] [Google Scholar]
  12. Kirsch J. F., Eichele G., Ford G. C., Vincent M. G., Jansonius J. N., Gehring H., Christen P. Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure. J Mol Biol. 1984 Apr 15;174(3):497–525. doi: 10.1016/0022-2836(84)90333-4. [DOI] [PubMed] [Google Scholar]
  13. Krause K. L., Volz K. W., Lipscomb W. N. Structure at 2.9-A resolution of aspartate carbamoyltransferase complexed with the bisubstrate analogue N-(phosphonacetyl)-L-aspartate. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1643–1647. doi: 10.1073/pnas.82.6.1643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lantwin C. B., Schlichting I., Kabsch W., Pai E. F., Krauth-Siegel R. L. The structure of Trypanosoma cruzi trypanothione reductase in the oxidized and NADPH reduced state. Proteins. 1994 Feb;18(2):161–173. doi: 10.1002/prot.340180208. [DOI] [PubMed] [Google Scholar]
  15. Lolis E., Alber T., Davenport R. C., Rose D., Hartman F. C., Petsko G. A. Structure of yeast triosephosphate isomerase at 1.9-A resolution. Biochemistry. 1990 Jul 17;29(28):6609–6618. doi: 10.1021/bi00480a009. [DOI] [PubMed] [Google Scholar]
  16. Lolis E., Petsko G. A. Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis. Biochemistry. 1990 Jul 17;29(28):6619–6625. doi: 10.1021/bi00480a010. [DOI] [PubMed] [Google Scholar]
  17. Mattevi A., Obmolova G., Kalk K. H., van Berkel W. J., Hol W. G. Three-dimensional structure of lipoamide dehydrogenase from Pseudomonas fluorescens at 2.8 A resolution. Analysis of redox and thermostability properties. J Mol Biol. 1993 Apr 20;230(4):1200–1215. doi: 10.1006/jmbi.1993.1236. [DOI] [PubMed] [Google Scholar]
  18. Mattevi A., Obmolova G., Sokatch J. R., Betzel C., Hol W. G. The refined crystal structure of Pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 A resolution. Proteins. 1992 Aug;13(4):336–351. doi: 10.1002/prot.340130406. [DOI] [PubMed] [Google Scholar]
  19. Mattevi A., Schierbeek A. J., Hol W. G. Refined crystal structure of lipoamide dehydrogenase from Azotobacter vinelandii at 2.2 A resolution. A comparison with the structure of glutathione reductase. J Mol Biol. 1991 Aug 20;220(4):975–994. doi: 10.1016/0022-2836(91)90367-f. [DOI] [PubMed] [Google Scholar]
  20. McPhalen C. A., Vincent M. G., Jansonius J. N. X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase. J Mol Biol. 1992 May 20;225(2):495–517. doi: 10.1016/0022-2836(92)90935-d. [DOI] [PubMed] [Google Scholar]
  21. Pai E. F., Schulz G. E. The catalytic mechanism of glutathione reductase as derived from x-ray diffraction analyses of reaction intermediates. J Biol Chem. 1983 Feb 10;258(3):1752–1757. [PubMed] [Google Scholar]
  22. Perry K. M., Fauman E. B., Finer-Moore J. S., Montfort W. R., Maley G. F., Maley F., Stroud R. M. Plastic adaptation toward mutations in proteins: structural comparison of thymidylate synthases. Proteins. 1990;8(4):315–333. doi: 10.1002/prot.340080406. [DOI] [PubMed] [Google Scholar]
  23. Wierenga R. K., Kalk K. H., Hol W. G. Structure determination of the glycosomal triosephosphate isomerase from Trypanosoma brucei brucei at 2.4 A resolution. J Mol Biol. 1987 Nov 5;198(1):109–121. doi: 10.1016/0022-2836(87)90461-x. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES