Introduction to Enzymes
Part V
Part V. Enzyme Framework - Why are Enzymes so Large?
We have discussed the formation of a protein's 3-D shape recall- the 4 levels of protein structure: Primary, Secondary, Tertiary, Quaternary. They make up a "Framework" to bring the AA side chains of the active site together. By bringing the AA side chains of the active site together they can act synergistically or in concert which is part of what makes enzymes very effective catalysts.
Figure 9. Ribonuclease with substrate RNA model bound in active site. His12 and His119 are involved in catalysis of the phosphodiester bond in the backbone of the RNA. Lys41 assists with binding the RNA molecule.
The active AA side chains also provide the enzyme with a high degree of specificity so that only certain substrates are bound to the enzyme's active site.
Figure 10. Model of RNA substrate bound to ribonuclease. On the top is shown the hydrogen bonding between Thr45 and the uracil group of the model RNA substrate. On the bottom is shown a close up of the model RNA substrate bound to the ball-and-stick model of ribonuclease with the H-bonds between the substrate uracil and the key Thr45 hydroxyl group and its alpha-amino group. Compare this figure to Fig. 9 where whole enzyme is shown.
Figure 9 & 10 from Zubay et al., Principles of Biochemsitry copyright ©1995 Brown Comm.
The concerted action of the AA side chains during catalysis also controls the formation of products so that only specific products are made and side reactions do not occur.
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©Wilbur H. Campbell, 1995; wcampbel@mtu.edu