There are two different ways of defining the "perfect" enzyme and both of them are wrong because there's no such thing. The common textbook definition picks up on the idea that the "perfect" enzyme catalyzes a reaction every time it encounters a substrate(s). These enzyme rates are referred to as "diffusion-controlled" rates since the rate is limited only by the rate at which substrate diffuses into the reaction site on the enzyme. Some enzymes can even catalyze reactions that are slightly faster than the diffusion-controlled limit.
Here's what Voet & Voet (4th edition) say (page 490) ...
Some Enzymes Have Attained Catalytic PerfectionAs I discussed in two previous posts, it's very misleading to refer to these enzymes as "perfect" enzymes since there are thousands of enzymes that get along just fine having evolved a pretty fast reaction rate that's far from the maximum value. They are good enough enzymes for the conditions of the cell. Who's to say that they haven't evolved a "perfect" solution to reaction rates even though it's not the fastest rate possible? [Better Biochemistry: The Perfect Enzyme] [Better Biochemistry: Good Enough Enzymes]. (The post on good enough enzymes has some nice data on average rate constants and average turnover numbers.)
Thus, enzymes with such values of kcat/Km must catalyze a reaction every time they encounter a substrate molecule. ... several enzymes ... have achieved this state of virtual catalytic perfection.
Better BiochemistryThe other way of defining a "perfect" enzyme is to look at something called "catalytic proficiency." That's the ratio of two rates: the maximum rate catalyzed by the enzyme and the spontaneous rate of the reaction in the absence of enzyme. (Recall that enzymes speed up reactions that will occur naturally.) There are lots of reactions that take place very, very, slowly in nature. Some of them have half-lives measured in millions or even billions of years.
Any enzyme that can catalyze such reactions at an appreciable rate is going to have a high catalytic proficiency [Enzyme Efficiency: The Best Enzyme] [The Best Enzyme]. These enzymes are better candidates for best enzymes but only one of them could be the "perfect enzyme"—if that were a meaningful term.
The leading candidate for the enzyme with the highest catalytic efficiency used to be orotidine 5′-phosphate decarboxylase (OMP decarboxylase), an enzyme involved in pyrimidine biosynthesis. That's almost certainly the enzyme that the professor wanted the students to find. However, an even better enzyme was discovered six years ago. It's uroporphyrin decarboxylase1 with at catalytic proficiency 10× higher than orotidine 5′-phosphate decarboxylase. I posted about it in 2008.
And here's how the information in that 2008 post got incorporated into the latest edition of my textbook.
There might be even more proficient enzymes that have been characterized since then. Does anyone know?
There's an ongoing debate among biochemistry teachers about the kind of information that typical students in an introductory course can handle. The students in our "honors" course can easily handle the information in this blog post but I'm not so sure about the students in our large "non-majors" course intended for students who aren't specializing in biochemistry. Some of my readers teach biochemistry. What do you think?
Image Credit: Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., Pearson Education Inc. page 175 [Pearson: Principles of Biochemistry 5/E]
1. Mutations in the gene for uroporphyrin decarboxylase are responsible for a common form of porphyria Porphyria cutana tarda]