PHOSPHOLIPASE A2

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STRUCTURE EXPLAINS FUNCTION: PHOSPHOLIPASE A2

Part II: Exploring Phospholipase A2 Structure using Mol*

Go “Back” to the structure summary page and click on the “Structure” tab to explore the 3D structure of this protein in more detail. Focus on the enzyme's active site, including the residues involved in phospholipid binding to the enzyme and the residues involved in the catalytic mechanism for the enzyme function. Please read all three questions before you start working on them individually to ensure that the figures you create for Q1 and Q2 visually support the explanation you provide for Q3.

I prepared two quick guides you might find helpful as you create your figures:
1. Saving your progress: https://docs.google.com/document/d/1HTTf2lq2l_83GHq7rTE_NiYVF8g8syMeEmTkQds _E40/edit?usp=sharing
2. Changing the colors of your visual representations. https://docs.google.com/document/d/1tkBFDdI0GjW8lWgnLyKNKRfdO13uNUZ58C7SnV3PYVA/edit?usp=sharing

Your figures for this assignment will be assessed on:

● How well your figures and annotations meet the prompt’s requirements
● Consistency between your annotated figure and the single-sentence legend you provided for the figure

Q3.1. Make an annotated figure showing all the amino acids and other elements, such as small ions, in Phospholipase A2, which are critical for substrate binding and their interactions with its substrate in this crystal structure.

Figure Requirements for your molecular story and suggested workflow:

Identify Key Elements: Explore the structure thoroughly to list all amino acid residues and small ions critical for substrate recognition and binding. Note the specific interactions these elements participate in.

Choose View Parameters:
● Select a focus point that captures the key binding elements effectively.
● Set an appropriate zoom level and angle to highlight these elements.
● Since the substrate is large, you may need to manually add interactions for full representation, as the standard 5Å zoom may miss some interactions.
● Remove any parts of the structure that might distract from the primary elements you’re presenting.
Choose Representations, Colors, and Labels:

Van der Waals interactions are the weakest interactions, adding only to stability at close contact distances. Their powerful impact on lipid stability comes from the increased number of such contacts in lipid-lipid or lipid-protein interactions.


  • To emphasize van der Waals interactions between Phospholipase A2 and the phospholipid and highlight these interactions clearly :
    • Use the space fill representation for amino acid residues on the protein involved in van der Waals interactions and label those residues with their one-letter code and residue number by placing the text on the corresponding side chain (no need to circle these residues)
    • Use the ball and stick representation for the phospholipid and a distinct color for the carbon atoms of the phospholipid to highlight.


All other interactions are distance and/or direction-specific.
  • To show the exact location of the atoms involved in these interactions.
    • Use the ball-and-stick representation for amino acid residues on the protein involved in interactions other than van der Waals interactions. Label them with their one-letter code and residue number by placing the label next to the circle you draw around these residues.
    • Mark and label all such interactions (no additional description, just the name of the interaction)
Figure Legend:
  • Write a short legend (max 2 sentences) that begins: “Figure 1 shows …”
  • Place this legend directly under your annotated figure, and ensure it concisely describes what the figure highlights.

Q3.2. Make an annotated figure that maps all the critical elements of the catalytic mechanism for Phospholipase A2 shown in Q3 onto the cobra-venom Phospholipase A2 in a complex with a transition-state analog (PDB ID:1POB)

Then, add and label all the important interactions that stabilize the location of catalytically important atoms for their corresponding roles in the enzyme mechanism, as shown in Q3. Refer to your answers to Q2.3, Q2.4, and Q2.5 to help guide your focus.

Figure requirements for your molecular story:
  • Use ball and stick representation for the amino acid side chains you are showing as well as the phospholipid (Keep the cartoon representation for the rest of the protein)
  • Use different colors for the phospholipid carbons and the protein carbons.
  • Remove any distracting elements. For a clearer view, you can create separate components for each amino acid you want to show using the create component tool after selecting the amino acid. This will allow you to turn off the focus components and retain the residues you are interested in on your canvas. Then you can manually add the interactions you want to show.
  • Label all the elements to which you would like to draw your viewer’s attention to meet the prompt’s requirements, including the phospholipase A2 cleavage site on the shown transition-state analog.
  • Add a short figure legend (max two sentences) below your annotated figure that begins: “Figure 2 shows …”

Q3.3 The schematic representation for the mechanism of hydrolysis catalyzed by Phospholipase A2 (PLA2) is shown on the right. Using this mechanistic information, as well as your experience on other enzyme mechanisms, we have reviewed so far in the course, describe in 5 sentences or less how PLA2 facilitates the cleavage of the fatty acyl group bound to the second carbon (sn-2) of the glycerol backbone in the phospholipid molecule. Provide specific structural evidence from your two figures to support your explanation. Note that since the phospholipid in the crystal structure is a transition state analog that cannot be cleaved, the atomic arrangement around the cleavage site is different than what you would expect from the natural substrate of PLA2.

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