Background

Cholesterol biosynthesis is composed of a series of enzymatically catalyzed reactions. Each step is catalyzed by one or more enzymes.

Your Mission

Complete the second step of the Cholesterol biosynthesis pathway, the conversion of HMG-CoA to Mevalonic acid, catalyzed by HMGCR. The complete reaction corresponds to the highlighted area in this figure:



  • Download the starter pathway here: met-1-second-start.gpml.
  • Launch PathVisio and open the dowloaded file via File > Open.

      • Add the metabolite

    • Select Metabolite from the Data Node palette in the Objects tab.
    • Click on the canvas to place the node.
    • Double-click on the node to open its properties.
    • Search for “mevalonic acid”; Choose any of the entries that just say “mevalonic acid” (in order of priority ChEBI, LIPIDMAPS, PubChem, CAS); Click OK to select the identifier, and then click OK again to close the node properties window.

      • Add and connect the conversion arrow

    • Select the mim-conversion arrow from the MIM interactions palette in the Objects tab.
    • Drag and drop anywhere on canvas to create the interaction.
    • Drag the plain end (start) of the interaction over a target area on the starting metabolite node (HMG-CoA).
    • Drag the arrow end (end) of the interaction over a target area on the ending metabolite node (mevalonic acid).
    • Right-click on the conversion interaction and select Add anchor, or select the conversion interaction and then use the keyboard shortcut Ctrl+R (Command+R on Mac), to add the anchor.

      • Add the gene product that catalyzes the conversion.

      Add the enzyme

    • Select GeneProduct from the Data Node palette in the Objects tab.
    • Click on the canvas to place the node.
    • Double-click on the node to open its properties.
    • Search for “HMGCR”; Choose any of the entries that just say “HMGCR”; Click OK.

      • Add and connect the catalysis arrow

    • Select the mim-catalysis arrow from the MIM interactions palette in the Objects tab.
    • Drag and drop anywhere on canvas to create the interaction.
    • Drag the plain end (start) of the interaction over a target area on the enzyme node.
    • Drag the catalysis end (end) of the interaction over the anchor on the conversion line.
    • (Optional) Align nodes using toolbar actions.
    • Done!
  • Save your work as a GPML file under File > Save As.
  • Drag-and-drop the GPML file below to check if it is correct.