This isn't breaking news (it's a Molecule of the Month for January 2001), but it is relevant to the study of enzymes and also, eventually, the study of metabolism. Go to http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb13_1.html

Use these diagrams for questions 1, 3, and 5.

1. Alcohol dehydrogenase catalyzes the reaction shown. Why is the structure of the alcohol shown with R rather than a specific structure?

2. Click on the link to PDB entry htb and first read the title of the Primary Citation. Then click on the link to the abstract and read the first two sentences. What does beta3beta3 mean?
How is the primary structure of beta3 different from beta1?

3. Draw an arrow to the part of NAD⁺ that has an interaction with the side chain of residue 369 and name the type of interaction.

4. How is the interaction of beta3 with NAD⁺ different from that of beta1?
How does this change the K_d for NAD⁺ with the enzyme? Answering this requires reading the rest of the abstract.

5. Why is 4-iodopyrazole one of the ligands used in determining the structure of the protein?

Answers:

1. Alcohol dehydrogenase catalyzes the reaction for a variety of different alcohols, ranging from methanol to retinol.

2. Beta3beta3 means that the enzyme consists of two identical chains, both beta3.
Beta1 has an arginine at position 369, and beta3 has a cysteine at position 369.

3. An electrostatic (ionic) interaction with the phosphoryl groups (PO₃^2-).

4. Beta3 loses the electrostatic interaction, although with 2 water molecules, it still has hydrogen bonds to the NAD⁺. The K_d from beta3 is much larger (350X as large) as that for beta1. (It's even larger for NADH–4000X).

5. 4-iodopyrazole is a competitive inhibitor of the enzyme, probably binding instead of an alcohol. This forms a stable structure because the NAD⁺ can't be converted to NADH and leave.

Comments after grading: One of the goals of the assignments is learning to convert the terms used in scientific papers into terms used in the class. For this reason, I'd like to discourage quoting verbatim from the articles.

So, for question 2, answering only "this is homodimeric alcohol dehydrogenase" actually doesn't provide more than a quote from the article without any indication of understanding what "homodimeric" means. It's also not very specific, as the alcohol dehydrogenase could be beta1beta1, sigma1sigma1, or any of several other possibilities.

Question 5 was clearly the most challenging. Inhibitors are often used for determining enzyme structures because an enzyme-inhibitor complex is more stable (lasts longer) than an enzyme-substrate complex. Answering that it helps provide information about enzyme-substrate interactions is a reasonable guess, although the abstract is clearly focusing much more on enzyme-NAD⁺ interactions.

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