Pathway Tools Workshop:
Protein complexes
Exercise 6: Polymerization

Please only modify the H. pylori database.
In this exercise we will create the polymeric compound levan, define a pathway that
uses it, and link an instance to a polymeric class in the pathway.
Fructan is a polymer of fructose molecules attached to a base sucrose unit. Levan is a
type of fructan where the fructose units are attached by β(2->6) bonds.
6-kestotriose: the simplest form of levan
The enzyme catalyzing the polymerization of levan from sucrose is called levansucrase
(EC 2.4.1.10):
sucrose + 1,2--D-glucosyl-(2,6-β-D-fructosyl)n = glucose + 1,2--D-glucosyl-(2,6-β-Dfructosyl)n +1
In order to describe the reaction, levan needs to be curated as a polymeric compound
class.
Part A: creating a polymeric reaction
Using the Ontology Browser, create a class for levan under the Fructans class. Use the
frame ID Levan (remember to enter it between vertical bars, i.e. |Levan|, so the software
will not convert the name to upper case).
1. Search for the existing compound class Fructans. Open it in the Ontology Editor.
2. Highlight the Fructans class, and create the new subclass by selecting Frame ->
Create -> Class. Give it the name |Levan| and click OK.
Figure 1: Creating a class for Levan using the Ontology Editor
3. Highlight the new class and open it in the frame editor by selecting
Frame -> Edit. Specify the common name “a levan” by highlighting the slot
COMMON-NAME, selecting Value -> Add Value, and typing the name.
Now follow this procedure to add the following polymeric names: for the slots "NNAME", "N+1-NAME" and "N-1-NAME" add the values
1,2-β-D-glucosyl-(2,6-β-D-fructosyl)_n
1,2-β-D-glucosyl-(2,6-β-D-fructosyl)_(n+1)
1,2-β-D-glucosyl-(2,6-β-D-fructosyl)_(n-1)
(see figure 2)
Figure 2: Assigning polymeric names in the Frame Editor
Close the Frame Editor by selecting Application -> Close
Close the Ontology Editor by selecting Application -> Quit GKB-Editor (then select
Save KB and quit).
4. Create the polymerization reaction, using the class name for both reactant and
product.
sucrose + Levan = glucose + Levan
Give the reaction the EC number 2.4.1.10, and mark it as an Official EC. Click OK.
5. Open the reaction frame in the frame editor, and locate the reactanst/products in
the LEFT and RIGHT slots (see figure 3).
Highlight “a levan” in the LEFT slot, and select Value -> Add Facet/Annot -> <new
annotation>. In the dialog box that appears type NAME-SLOT and press OK. In the
next dialog box type N-NAME and press OK again.
Repeat for “a levan” in the RIGHT-SLOT, but this time type N+1-NAME in the final
dialog box.
When done, close the editor by selecting Application -> Close
Figure 3: Adding NAME-SLOT annotations to the polymeric substrates of a reaction, using the
Frame Editor
Congratulations! At this point you have finished specifying a new polymerization
reaction.
Tip: You have created a new compound class. If the DB contains instances that should
reside in the new class, remember to move them into it using the Ontology Editor or the
classification button in the Compound Editor.
Part B: Adding the polymerization reaction to a pathway:
1. Create a reaction as follows:
2 sucrose = D-glucose + a levan.
Give it the official EC number 2.4.1.99.
2. Create a new pathway, call it “fructan biosynthesis”, and classify it under
Biosynthesis -> Carbohydrates -> Sugars. Add the two reactions that you created as
described in figure 4.
Figure 4: Fructan biosynthesis pathway
3. Open the pathway frame in the Frame Editor
4. Right click on the last compound in the pathway, and select “Create Polymerization
Link”. Exit saving your changes. The pathway should look like the one in figure 5.
Figure 5: Fructan biosynthesis pathway with a polymerization link
5. Note that it is possible to specify which polymeric name is shown in the pathway. For
example, you can have the reaction appear as (n-1) going to (n). To do so, open the
pathway in the Pathway Editor, right click on the compound class and select “Assign
Polymerization Name”.
Part C: Linking an instance to a polymeric class
1. Create a new compound with the common name 6,6-kestotetraose (this is a type of a
levan sugar, with four fructose units connected to the glucose unit). Classify the
compound in the Levan class (all carbohydrate -> a carbohydrate -> a sugar -> a
polysaccharide -> a fructan -> a levan).
2. Note the frame ID of the polymerization reaction and the instance that should be
linked to it. Determine if the compound should be linked to the reactant or the product
of the reaction.
In my case, the reaction frame-ID is RXNI-106, and the instance (6,6-kestotetraose)
frame ID is CPD-9550. Most likely, the objects will have different frame IDs in your
DBs.
3. Open the pathway in the Frame Editor.
4. Highlight the slot "CLASS-INSTANCE-LINKS"
5. Click Value -> Add Value and enter the frame ID of the polymerization reaction
6. Highlight the new value and click: Value -> Add Facet/Annot -> <new annotation>
Enter PRODUCT-INSTANCES (if you want to link the instance to a reactant of the
reaction, use REACTANT-INSTANCES instead) in the dialog box that appears and
click OK. Enter the frame ID of the instance that should be linked to the
polymerization reaction in the next dialog box. Click OK. It should look similar to
Figure 6.
7. Exit the Frame Editor and open the Pathway Editor
Figure 6: Adding a Class-Instance link
Figure 7: the final pathway