Skip to main content
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1994 Aug;3(8):1344–1346. doi: 10.1002/pro.5560030821

A new family of carbon-nitrogen hydrolases.

P Bork 1, E V Koonin 1
PMCID: PMC2142920  PMID: 7987228

Abstract

Using computer methods for database search and multiple alignment, statistically significant sequence similarities were identified between several nitrilases with distinct substrate specificity, cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function. All these proteins appear to be involved in the reduction of organic nitrogen compounds and ammonia production. Sequence conservation over the entire length, as well as the similarity in the reactions catalyzed by the known enzymes in this family, points to a common catalytic mechanism. The new family of enzymes is characterized by several conserved motifs, one of which contains an invariant cysteine that is part of the catalytic site in nitrilases. Another highly conserved motif includes an invariant glutamic acid that might also be involved in catalysis.

Full Text

The Full Text of this article is available as a PDF (365.8 KB).

Selected References

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

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank, recent developments. Nucleic Acids Res. 1993 Jul 1;21(13):3093–3096. doi: 10.1093/nar/21.13.3093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cluness M. J., Turner P. D., Clements E., Brown D. T., O'Reilly C. Purification and properties of cyanide hydratase from Fusarium lateritium and analysis of the corresponding chy1 gene. J Gen Microbiol. 1993 Aug;139(8):1807–1815. doi: 10.1099/00221287-139-8-1807. [DOI] [PubMed] [Google Scholar]
  4. Gish W., States D. J. Identification of protein coding regions by database similarity search. Nat Genet. 1993 Mar;3(3):266–272. doi: 10.1038/ng0393-266. [DOI] [PubMed] [Google Scholar]
  5. Higgins D. G., Bleasby A. J., Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. doi: 10.1093/bioinformatics/8.2.189. [DOI] [PubMed] [Google Scholar]
  6. Kobayashi M., Izui H., Nagasawa T., Yamada H. Nitrilase in biosynthesis of the plant hormone indole-3-acetic acid from indole-3-acetonitrile: cloning of the Alcaligenes gene and site-directed mutagenesis of cysteine residues. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):247–251. doi: 10.1073/pnas.90.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Kobayashi M., Yanaka N., Nagasawa T., Yamada H. Primary structure of an aliphatic nitrile-degrading enzyme, aliphatic nitrilase, from Rhodococcus rhodochrous K22 and expression of its gene and identification of its active site residue. Biochemistry. 1992 Sep 22;31(37):9000–9007. doi: 10.1021/bi00152a042. [DOI] [PubMed] [Google Scholar]
  8. Koonin E. V., Bork P., Sander C. Yeast chromosome III: new gene functions. EMBO J. 1994 Feb 1;13(3):493–503. doi: 10.1002/j.1460-2075.1994.tb06287.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Nagasawa T., Mauger J., Yamada H. A novel nitrilase, arylacetonitrilase, of Alcaligenes faecalis JM3. Purification and characterization. Eur J Biochem. 1990 Dec 27;194(3):765–772. doi: 10.1111/j.1432-1033.1990.tb19467.x. [DOI] [PubMed] [Google Scholar]
  10. Rohde K., Bork P. A fast, sensitive pattern-matching approach for protein sequences. Comput Appl Biosci. 1993 Apr;9(2):183–189. doi: 10.1093/bioinformatics/9.2.183. [DOI] [PubMed] [Google Scholar]
  11. Rost B., Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993 Jul 20;232(2):584–599. doi: 10.1006/jmbi.1993.1413. [DOI] [PubMed] [Google Scholar]
  12. Schuler G. D., Altschul S. F., Lipman D. J. A workbench for multiple alignment construction and analysis. Proteins. 1991;9(3):180–190. doi: 10.1002/prot.340090304. [DOI] [PubMed] [Google Scholar]
  13. Willison J. C. Biochemical genetics revisited: the use of mutants to study carbon and nitrogen metabolism in the photosynthetic bacteria. FEMS Microbiol Rev. 1993 Jan;10(1-2):1–38. doi: 10.1111/j.1574-6968.1993.tb05862.x. [DOI] [PubMed] [Google Scholar]

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

RESOURCES