Practical 1

Genome-Scale Metabolic Databases

Later in the course we will be looking at one of the alternatives to the Embden-Meyerhof pathway of glycolysis: the Entner-Doudoroff pathway. In E. coli this is used to metabolize gluconate, found in the intestinal lining. In Zymomonas mobilis, the phosphorylated Entner-Duodoroff pathway is used for a very rapid fermentation of glucose to ethanol. Here, you will use the web interfaces to some of the major metabolism and enzyme databases to find out about the enzymes and reactions of the pathway.
A limitation of the pathway paradigm of metabolism is that it singles out a highly context-dependent subset of the metabolic network, and you will come across some of the unfortunate consequences of this in this exercise. For some background to the metabolism of Z. mobilis, see the articles here and here.

For each of:
- MetaCyc and
- KEGG
  - carry out a pathway search for "Entner". Compare with the network diagram in one of the two papers. Can you orientate yourself? Does it show everything you need?
Eventually you will build a model containing all the reactions from glucose to ethanol by specifying the enzymes available to Z. mobilis. Starting from the MetaCyc and KEGG pathway maps, navigate down to the pages detailing the enzyme properties and reactions linked to the enzyme names and EC numbers.
Note that both databases have cross-references to other data sources on enzymes, of which ENZYME or IntEnz are the sites with the official classification of enzymes by EC numbers, and BRENDA is a compendium of enzyme properties culled from the literature for each EC number.
Can you find the EC number of a glucose-6-phosphate dehydrogenase that accepts both NAD and NADP as oxidising agents, as the enzyne in Z. mobilis does?
What is the net yield of ATP from conversion of one glucose to ethanol by this route?
If you want to know more about the Enzyme Classification numbers, this site will more than satisfy your curiosity.