C. Douglas Hershberger

The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolic enzymes and their organization into metabolic pathways. Currently, it contains information on over 400 enzymes. In the last year the enzyme page was enhanced to contain more internal and external links; it also displays the different metabolic pathways in which each enzyme participates. In collaboration with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology, 35 UM-BBD enzymes were assigned complete EC codes during 2000. Bacterial oxygenases are heavily represented in the UM-BBD; they are known to have broad substrate specificity. A compilation of known reactions of naphthalene and toluene dioxygenases were recently added to the UM-BBD; 73 and 108 were listed respectively. In 2000 the UM-BBD is mirrored by two prestigious groups: the European Bioinformatics Institute and KEGG (the Kyoto Encyclopedia of Genes and Genomes). Collaborations with other groups are being developed. The increased emphasis on UM-BBD enzymes is important for predicting novel metabolic pathways that might exist in nature or could be engineered. It also is important for current efforts in microbial genome annotation.

The University of Minnesota Biocatalysis/Biodegradation Database: microorganisms, genomics and prediction

The University of Minnesota Biocatalysis/Biodegradation Database (http://www.labmed.umn.edu/umbbd/ ) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reactions, 600 compounds and 400 enzymes, and containing approximately 250 microorganism entries. It includes information on most known microbial catabolic reaction types and the organic functional groups they transform. Having reached its first goals, it is ready to move beyond them. It is poised to grow in many different ways, including mirror sites; fold prediction for its sequenced enzymes; closer ties to genome and microbial strain databases; and the prediction of biodegradation pathways for compounds it does not contain.

The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://www.labmed.umn.edu/umbbd/i nde x.html) first became available on the web in 1995 to provide information on microbial biocatalytic reactions of, and biodegradation pathways for, organic chemical compounds, especially those produced by man. Its goal is to become a representative database of biodegradation, spanning the diversity of known microbial metabolic routes, organic functional groups, and environmental conditions under which biodegradation occurs. The database can be used to enhance understanding of basic biochemistry, biocatalysis leading to speciality chemical manufacture, and biodegradation of environmental pollutants. It is also a resource for functional genomics, since it contains information on enzymes and genes involved in specialized metabolism not found in intermediary metabolism databases, and thus can assist in assigning functions to genes homologous to such less common genes. With information on >400 reactions and compounds, it is poised to become a resource for prediction of microbial biodegradation pathways for compounds it does not contain, a process complementary to predicting the functions of new classes of microbial genes.

Biocatalysis and Biodegration

Help your students save on textbooks! Email us and receive a coupon to share with your students for 20% off of the purchase of a print copy. Designed for use as a textbook in courses in biodegradation, this important new volume details both the fundamental concepts of the microbial transformation of organic compounds as well as its application for biotechnology and biodegradation. It offers comprehensive coverage of microbial catabolism from the group that developed the Biocatalysis/Biodegradation database on the Web and discusses the logic of catabolism use in predicting biodegradation. Hardcover, 379 pages, illustrations, index.