Discovering New Biocatalytic Reactions: Learning the University of Minnesota Biocatalysis / Biodegradation Database (UM-BBD) and the Biocatalysis Literature

Goal: Find documented scientific literature describing the microbial metabolism of a compound containing a chemical functional group(s) not presently contained within the UM-BBD.

1. Go to the UM-BBD "functional group" web page and "biochemistry of the elements"
   • Function Groups in UM-BBD:
     • Table = http://umbbd.ahc.umn.edu/search/FuncGrps.html
     • Figure = http://umbbd.ahc.umn.edu/search/FG_image_map.html
   • Biochemical Periodic Table = http://umbbd.ahc.umn.edu/periodic/


2. Consider other chemical functional groups that are:
   1. not presently depicted on the UM-BBD
   2. stable in water unless transformed by a suitable catalyst (enzyme)


3. Search:
   1. Medline
   2. SciFinder
   3. Information on using bibliographic resources:
   • Lynda Ellis, "Bibliographic Searching in the Bioinformatic Sciences"
   • Lynda Ellis, "Formulating Entrez Searches for Compounds, Enzymes and Genes"
   
   
   • When searching, make sure to use the terms: "name of functional group" AND "bacteria" AND "metabolism"


4. Compile information:
   1. reference citations, including PMID numbers if possible
   2. reactants
   3. products
   4. cofactors
   5. enzyme name
   6. enzyme EC number
   7. genes


5. Provide information by e-mail via the submission form to:
   • Prof. Wackett, wackett@biosci.cbs.umn.edu
   • Prof. Ellis, lynda@mail.ahc.umn.edu
   • Here is the submission form to use: http://cbs.umn.edu/labs/wackett/wacweb/locallinks/umbbd-mailform.html