In many cases, new enzymes evolve from primitive enzymes that catalyzed similar reactions [see The Evolution of Enzymes from Promiscuous Precursors]. It's quite easy to see how this could happen by gene duplication and there are tons of examples.
But what about the first primitive enzymes themselves? Presumably, they evolved all on their own. When scientists think of this problem, they usually think in terms of evolving a specific modern enzyme. This looks like a long shot, similar to the probability that a specific person will win the lottery tomorrow. What they don't realize is that this is an unnecessarily restrictive scenario.
There are many possible ways of catalyzing a given metabolic reaction. What we see today is the "lucky winner"—the one enzyme that happened to win the lottery. There were many other possible enzymes that could have evolved and that makes the overall probabilities much more reasonable. There could be a million structurally distinct proteins capable of catalyzing a particular reaction. What you should be thinking about is the probability that any one of those possible enzymes will evolve and not the probability that a specific enzyme will evolve. It's like calculating the probability that anyone in a large city will win the lottery—a much more reasonable number.
Aldolase in Gluconeogenesis & Glycolysis]. That example is covered in every biochemistry textbook.
There are also examples of parallel evolution in the citric acid cycle. At the beginning of the cycle, for example, there are two completely different enzymes catalyzing the formation of acetyl-CoA [Some Bacteria Don't Need Pyruvate Dehydrogenase]. Several other reaction in the pathway are catalyzed by different enzymes in different species of bacteria.
This suggests that early forms of life evolved several different enzymes for the same reaction although one of them might have taken over because it was more efficient (or lucky). Eugene Koonin calls this non-orthologous gene displacement (NOGD) and it's one of the reasons why the set of genes common to all species is surprisingly small [The Core Genome].
It's been known for a long time that cyanobacteria are missing one of the common enzymes of the citric acid cycle. It's enzyme #4 in the figure at the top of the post. The common name of this enzyme is α-ketoglutarate dehydrogenase but nowadays it's called by its more formal name in the scientific literature: 2-oxoglutarate dehydrogenase. Cyanobacteria also exhibit low levels of enzyme #5 in the pathway; succinly-CoA synthetase.
Together, these two enzymes catalyze these reactions.
A recent paper by Zhang and Bryant (2011) reports on the discovery of two new enzymes in cyanobacteria: α-ketoglutarate decarboxylase and succinic semialdehyde dehydrogenase. Together these two new enzyme catalyze the conversion of α-ketoglutarate to succinate. What this means is that cyanobacteria can complete the citric acid cycle using two enzymes that are completely different than the ones used in most other species. It's another example of parallel evolution.
This is one more example of the evolution of different enzymes catalyzing the same reaction. It's further evidence that the earliest forms of life may have evolved lots of different enzymes with similar functions and it suggests that the specific enzymes we see today are just the lucky ones that arose first. There were many other possible enzymes that could have done the job just as well.
[Photo Credit: Cyanobactreria]
Zhang, S., and Bryant, D.A. (2011) The tricarboxylic acid cycle in cyanobacteria. Science 334:1551-1553. [PubMed] [DOI: 10.1126/science.1210858]