The Internet Workbook

Net Problem #1

Identify similarities between glycolytic enzymes

As you learned in earlier units, there are a limited number of protein architectures. It has been hypothesized that enzymes that have similar architectures may be evolutionarily related to one another. In theis section we are going to discover which glycolytic enzymes have simiar architectures. One of the resources we will use for this is SCOP, the Structural Classification of Proteins.

Summary: SCOP is a great way to start research about protein structure. It is mirrored in a variety of locations so the service will always be relatively quick. It has extensive online help, is thoroughly cross-referenced with PDB, and is laid out in such a way that it is very easy to find what you are looking for, no matter if you have a sequence, a species name, or neither.

Developed by the MRC Laboratory of Molecular Biology and Centre for Protein Engineering at Cambridge University, SCOP is a comprehensive database containing information on all proteins whose structure is known. The goal of the database is to be able to compare structural similarities between proteins and, therefore, determine if there is a common evolutionary origin. SCOP contains all of the proteins that are located in the Protein Data Bank and offers differing representations of proteins in links to PDB entries, images, and sequences.

Be sure to read through this section completely before doing this exercise. You may want to print out a copy of this exercise prior to going to SCOP.

Go to SCOP. Choose the US server closest to your location for fastest results:
- East Coast, USA http://www.pdb.bnl.gov/scop/
- West Coast, USA http://scop.stanford.edu/scop/
You are going to "run a keyword search" against SCOP. That is, you're going to ask SCOP what it knows about some of the proteins that are associated with glycolysis.
Type in "glyceraldehyde" (it is often easiest to query SCOP with single keywords, and then to pare down answers to what you want). You should see a host of returns. Are any of them glyceraldehyde-3-phosphate dehydrogenase? If so, go to this family.
Look at how SCOP has organized information:
1. Root
2. Class
3. Fold
4. Superfamily
5. Family
  You are currently at the 'family' level. You can go up or down in the 'hierarchy.' Let's drop down a few nothces: click on one of the enzymes within this family, the human enzyme. You'll see that we now have a few new levels of information:
6. Protein
7. Species
This is as deep as SCOP goes. However, we can now examine the individual enzyme. Click on "3gpd." This is a file with structural information about the enzyme. Later, you'll learn how to access this structural information in different ways, and how to look at the enzyme structures themselves.
For right now, let's do what SCOP is best at, classifying proteins. Back out of the file until you get to the "species" level of SCOP: all seven categories we have talked about should be displayed. Now, click on a higher level, such as "superfamily."
SCOP shows you what families of enzymes are most related. The GAPDH family is most structurally similar to the dihydropicolinate reductase and glucose-6-phosphate dehydrogenase families. Does this make sense? Partially: while glyceraldehyde may not be much like dihydropicolinate or glucose, all of the enzymes in this superfamliy carry out redox reactions.
Now let's move up another couple of notches, to the "fold." There are lots of enzyme superfamilies and families with the general [alpha + beta] fold (that is, that have segregated as opposed to interspersed alpha helices and beta sheets).
Now that we have some familiarity with the hierarchy, let's move around and ask questions about other glycolytic enzymes. Go to the keyword search (located at the bottom of the page), and type in "triose" (a good keyword for the enzyme triose phosphate isomerase (TIM); why might this be a better keyword than either phosphate or isomerase?).
Write down the family, superfamily and fold of TIMs. You will hand this in to your instructor.
Now do the same for pyruvate kinase. Can you figure out what keyword(s) to use for this enzyme? You should be on a page with a lot of entries. Look through the entries for the rabbit enzyme. How many times is it listed? Go back and forth between the different entries; their titles are the same, but are they the same? Why? What differentiates them?
Write down the family, superfamily, and fold of the rabbit domains. Is any part of the rabbit protein similar to another glycolytic enzyme? You will hand this in.
Now draw your own hierarchy for the relationship between the TIM and pyruvate kinase proteins, based on the SCOP classifications. You will hand this in.
Finally, you can confirm SCOP's classifications for yourself. View the structure of TIM. Rotate the structure around. Now do the same for pyruvate kinase. Can you see similarities between their barrels?

Last updated: July 18, 1998
URL: http://biotech.icmb.utexas.edu/glycolysis/wwwquest1.html
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