What's an EC Number & how to interpret it

THE ZYMVOL BLOG

What's an EC Number & how to interpret it

You might have heard about EC numbers.

They are widely used in biochemistry and molecular biology to provide a clear and standardized way to refer to enzymes, especially in scientific literature and databases.

This classification method helps us differentiate among thousands of enzyme types that, otherwise, would be very hard to recognise by everyone.

Because giving enzymes arbitrary, common names worked well when only a few were known.

But now, after more than a century of enzyme discovery, naming more than 8.000 enzymes would be simply impossible.

Only a few names have survived in our common language, such as cellulase (EC 3.2.1.4), papain (EC 3.4.22.2) or proteases (all EC 3.4. numbers). For the rest, EC numbers are our only and best way to talk about the broad world of biocatalysis.

 

What’s an EC Number?

The Enzyme Commission (EC) number is a nomenclature system based on the chemical reactions that these proteins catalyze.

It was developed by the International Union of Biochemistry and Molecular Biology (IUBMB) and consists of a numerical classification scheme where each number is associated with an enzyme-catalyzed reaction.

Note that each EC number is not associated with a specific enzyme, because in nature we can find different enzymes that catalyze the same reaction.

 

How to read an EC number

An EC number is typically represented as a sequence of four numbers separated by periods, which is linked to a recommended name. For example, EC 1.1.1.1 (alcohol dehydrogenase).

Let’s see what each of these four numbers represents:

First Number: The type of reaction or enzyme class

The first number indicates the enzyme class, based on the type of reaction each of these classes catalyzes. There are seven main classes:

EC 1: Oxidoreductases – Enzymes that catalyze oxidation-reduction reactions.

EC 2: Transferases – Enzymes that transfer a functional group (e.g., a methyl or phosphate group).

EC 3: Hydrolases – Enzymes that catalyze the hydrolysis of various bonds.

EC 4: Lyases – Enzymes that break various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or ring structure.

EC 5: Isomerases – Enzymes that catalyze the transfer of groups within molecules to yield isomeric forms.

EC 6: Ligases – Enzymes that join two molecules together, typically using ATP.

EC 7: Translocases – Enzymes that catalyze the movement of ions or molecules across membranes or their separation within membranes.

Second and third numbers: Enzyme subclass and sub-subclass

These two numbers provide more detail about the type of molecular group, bond or product involved in the enzyme-catalyzed reaction, narrowing down the specificity of the reaction.

Fourth Number: Enzyme identification

This is the serial number of the enzyme. It represents the specific enzyme identity, related to specific metabolites and/or cofactors involved in the enzyme-catalyzed reaction.

 

A couple of examples

Now that you know the basics, let’s see how this looks put into practice.

Let’s start with the first number that appears in the classification:

 

EC 1.1.1.1

– The first «1» indicates that it’s an oxidoreductase (an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, to another, the oxidant).

– The second «1» specifies that it acts on the CH-OH group of donors.

– The third «1» indicates that NAD+ or NADP+ is the acceptor.

– The final «1» is the specific serial number for this enzyme in its group, which is given the recommended name of alcohol dehydrogenase.

 

See? That wasn’t so hard.

Now let’s mix it up a little and look at another one.

 

EC 6.3.2.24

– Here, the first «6» indicates that it’s a ligase (an enzyme that catalyzes the joining of two molecules by forming a new chemical bond).

– The second number is «3» and specifies that the type of bonds that forms are carbon-nitrogen.

– The third number is «2» and specifies that the types of molecules that are bonded are an acid and an amino-acid.

– The last number is «24», the specific serial number for this enzyme in its group, and specifies that the two amino acids bond catalyzed by the enzyme is tyrosine—arginine, which gives the recommended name of tyrosine—arginine ligase.

 

Are you starting to get the hang of it? This classification is quite easy to follow. And, don’t worry, nobody expects you to know all these numbers by heart. You just need to understand the rationale behind. After all, EC numbers are here to make our lives easier!

 

Is there a complete enzyme classification by EC number?

Of course! People have always loved to bring order to chaos.

In this case, it is the IUBMB who provides an approved and updated enzyme classification list based on the EC number nomenclature: the ExplorEnz Enzyme Database.

The first edition was published in 1992. From then on, 29 more supplements or edits have been added to that initial version to register all the new enzymes discovered and modifications needed.

You can dive into its tree structure, expanding each list of the classes, subclasses, sub-subclasses and serial numbers, to have a deeper view of the entire classification.

 

How to find the enzyme that I’m searching for?

If you’ve ever had to find out if a certain reaction can be performed enzymatically, you may know the answer does not come easily navigating through the EC numbers database on your own.

This is a very common problem for industries or research groups considering the possibility of doing a chemical process with enzymes, who usually spend too much time searching in the literature or asking other colleagues.

In those cases, a quick and simple answer in the form of an EC number can save a lot of time and open the door to innovative projects that were long stuck.

At ZYMVOL we developed ZYMSCAN with that in mind: if a chemist wants to know if their reaction can be done enzymatically, they just have to submit their reaction and ZYMSCAN will confirm if it can be done with biocatalysis. In case it can, they will receive an email with the EC number of the enzyme family that matches the reaction.

 

As you can see, an EC number can be very useful not only in scientific literature, but also in applied chemistry; and now you know how to interpret it!


Introducing ZYMSCAN: the fastest way to check if there’s an enzyme for your reaction

COMPANY NEWS

Introducing ZYMSCAN:

the fastest way to check if there’s an enzyme for your reaction

Take me to ZYMSCAN

“Is there an enzyme for my process?”

We can’t tell you how many times we’ve been asked this question.

Trying to change your traditional chemical process for an improved biochemical one can be a pain. And this is not surprising at all, given how time-consuming the search of an enzyme for a specific reaction can be. 

The reality is, the individuals that could benefit most from applying enzymes are chemists. However, many are lacking the resources to answer the fundamental question: «Can I do this reaction with an enzyme?»

That’s why today we are happy to announce the launch of a new platform that will make your life easier: ZYMSCAN.

From now on, you are just a few clicks away from knowing if biocatalysis is right for you.

Oh, and have we mentioned that it is free?

Keep reading to learn more.

 

What is ZYMSCAN?

ZYMSCAN is a free, online tool for users who want to know if a certain reaction can be performed enzymatically without wasting time going through other methods.

 

How does it work?

Using ZYMSCAN is easy. Instead of spending weeks looking for your answer, just follow these three simple steps:

1) Fill out the form and submit the substrate and product of interest in SMILES format.

2) Zymvol will use its computational technology to scan the whole enzyme family landscape in search for the right fit. Our experts will accompany the process to certify the final answer.

3) Receive an email between 1-2 business days with the EC number of the enzyme family found.

Don’t worry, we’ve got you covered.
Just draw your molecule in the editor and we’ll create the SMILES for you.

Don’t know how a SMILES works? Check out some examples.

 

Who is ZYMSCAN for?

– Chemists, Innovation Managers or just about anyone who wishes to implement greener processes and products, but need to know first if it can be performed by enzymes.

– Academics or Universities whose research is related to enzymes.

 

Why did we create ZYMSCAN?

Let’s face it: the way many companies pursue biocatalysis today is not always efficient.

How much time do you waste searching for an enzyme? Going through the literature and asking for help, trying to find out if there’s one for the reaction you need?

We realized this was a common problem not only for our clients, but for many other companies looking to “go bio”.

With so many promising projects getting stuck in this first step, we knew it was important to launch a platform that was simple, quick, free of charge and supported by our experts.

If more companies can know from the get-go if there is an enzyme for their processes, we can speed up the transition to a better and greener chemistry everywhere.

Don’t know what reaction to try out?
Use our random SMILES generator!

 

Why does it take 1 business day to receive results?

To ensure optimal performance, ZYMSCAN’s results are obtained through a mix of automated computational work as well as human curation.

After sending your request, our proprietary Artificial Intelligence software does the search and rapidly matches the input substrate and product with an enzyme family. Afterwards, ZYMVOL experts take care of doing a final check on the information, to guarantee that the answer is as accurate as possible.

 

Will there be more updates coming soon?

ZYMSCAN is currently in beta phase, which means it is currently undergoing updates and improvements. As a result, you may encounter incomplete sections, minor disruptions, or changes in content.

We appreciate your patience while these updates are taking place. If you encounter any errors and wish to report them, please send us an email at info@zymvol.com.

Ready to try ZYMSCAN?