This is the three dimensional structure of the enzyme catalase that leads to a dramatic enhancement in the rate of decomposition of H₂O₂.

The enzyme acts as a catalyst for the reaction:

2 H₂O₂(aq) ----> 2 H₂O(l) + O₂(g)
ΔG^o_r = -103 kJ/mol, ΔH^o_r = -95 kJ/mol

it is one of the most efficient enzyme catalysts known as judged by its k_cat/K_M which is 4 x 10⁹ M^-1 s^-1.

You can find the file yourself on the Protein Databank Website (www.pdb.org) - this is the first X-ray structure of catalase and has the PDB entry 8CAT.

This color representation of the three dimensional configuration helps us visualize the structure of the protein (virtually all enzymes are protein polymers). The protein is made up of two "chains" and two additional co-factor molecules called hematins (these are shown in green with all atoms shown as spheres for emphasis). Two NADPH molecules are also bound. The catalytic reaction actually takes on the hematin groups, and so this part of the enzyme is called the active site.

If this is your first time using 3D viewing of protein structure using Jmol, experiment with the following:

You can change the way the protein is displayed (e.g. to stop the molecule rotating) by placing your mouse over the structure and bringing up the menu by right clicking (or double click on the Jmol logo). For example, on the menu you will see Spin > Stop. You can then grab the protein with the left mouse button and rotate the molecule to any view you desire. You can choose to look at the structure in different ways. Under the menu option "Style > Scheme", try "CPK Spacefill" or "Wireframe". These options show all the atoms that make up the protein (over 8000 in all).

For more advanced viewing options, you'll want to try out scripting. This way you can render different parts of the protein, its cofactors or substrates in different ways. To start, bring up the console on the menu. You'll need to search for a Jmol tutorial on what commands can be used.

For more information on the mechanism of catalase action on peroxides, see original references provided with the 8CAT entry in the Protein Databank. For general background, see a text like L. Stryer, "Biochemistry" (1995). Catalysis information in Vainshtein et al, Nature 293, 411 (1981)

Stephen E Bradforth, USC. November, 2000; revised November 2011.