Abstract
Two sequence-related subfamilies of flavin-binding beta/alpha-barrels have been identified (the type I and type II proteins) that differ in the nature of residue packing in the core of the barrel domain. Similar observed differences in the packing of internal amino acid side chains in beta/alpha-barrels have previously been used to argue that these domains have evolved convergently toward a stable structural framework. Using structural alignments of flavin-binding barrel proteins, we demonstrate that simple genetic alterations may be responsible for switching the nature of side-chain packing observed in beta/alpha-barrels. The implication is that the 2 structural classes of beta/alpha-barrel cores can arise divergently from an ancestral barrel framework and that convergent evolution to a stable fold need not be invoked to account for the emergence of 2 classes of beta/alpha-barrel core.
Full Text
The Full Text of this article is available as a PDF (3.7 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Boyd G., Mathews F. S., Packman L. C., Scrutton N. S. Trimethylamine dehydrogenase of bacterium W3A1. Molecular cloning, sequence determination and over-expression of the gene. FEBS Lett. 1992 Aug 24;308(3):271–276. doi: 10.1016/0014-5793(92)81291-s. [DOI] [PubMed] [Google Scholar]
- Farber G. K., Petsko G. A. The evolution of alpha/beta barrel enzymes. Trends Biochem Sci. 1990 Jun;15(6):228–234. doi: 10.1016/0968-0004(90)90035-a. [DOI] [PubMed] [Google Scholar]
- Lesk A. M., Brändén C. I., Chothia C. Structural principles of alpha/beta barrel proteins: the packing of the interior of the sheet. Proteins. 1989;5(2):139–148. doi: 10.1002/prot.340050208. [DOI] [PubMed] [Google Scholar]
- Lindqvist Y. Refined structure of spinach glycolate oxidase at 2 A resolution. J Mol Biol. 1989 Sep 5;209(1):151–166. doi: 10.1016/0022-2836(89)90178-2. [DOI] [PubMed] [Google Scholar]
- Phillips D. C., Sternberg M. J., Thornton J. M., Wilson I. A. An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase. J Mol Biol. 1978 Feb 25;119(2):329–351. doi: 10.1016/0022-2836(78)90440-0. [DOI] [PubMed] [Google Scholar]
- Scrutton N. S. alpha/beta barrel evolution and the modular assembly of enzymes: emerging trends in the flavin oxidase/dehydrogenase family. Bioessays. 1994 Feb;16(2):115–122. doi: 10.1002/bies.950160208. [DOI] [PubMed] [Google Scholar]
- Wilmanns M., Hyde C. C., Davies D. R., Kirschner K., Jansonius J. N. Structural conservation in parallel beta/alpha-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry. 1991 Sep 24;30(38):9161–9169. doi: 10.1021/bi00102a006. [DOI] [PubMed] [Google Scholar]
- Xia Z. X., Shamala N., Bethge P. H., Lim L. W., Bellamy H. D., Xuong N. H., Lederer F., Mathews F. S. Three-dimensional structure of flavocytochrome b2 from baker's yeast at 3.0-A resolution. Proc Natl Acad Sci U S A. 1987 May;84(9):2629–2633. doi: 10.1073/pnas.84.9.2629. [DOI] [PMC free article] [PubMed] [Google Scholar]