If you have used BioCyc, you probably noticed that many reactions have EC numbers printed next to them. EC numbers are everywhere – in the primary literature, in annotated genomes, in databases, in online encyclopedias. Where do they come from and what exactly do they mean?
A Bit of History
In the early days the naming of enzymes was not systematic.
As a result, many different enzymes were given the same name and, on the other hand,
several different names were assigned to the same enzyme. Many of the names
were not particularly helpful; for example, the enzyme now known as EC 1.6.99.1,
NADPH dehydrogenase, was originally named “old yellow enzyme”.
To sort out the mess, Dixon and Webb introduced a
classification system in their 1958 book “Enzymes”, which was based on the
reaction catalyzed by the enzyme. Although it was rather limited, it provided
the foundation for the current classification system. At about the same time,
the International Union of Biochemistry has decided to form an official international
commission on enzymes to develop a better classification and naming system. The
first full report of the commission was published in 1965, using a six-category
system that is still used today. Although this is not the place to describe
classification principles, in general each enzyme receives a unique
four-component identification number that not only identifies it, but also
provides insight into the enzymatic activity of the enzyme. Each EC entry
provides additional information such as lists of names and synonyms,
references, and often commentary. Full details about the principles of the classification
system can be found at http://enzyme-database.org/rules.php
and https://en.wikipedia.org/wiki/Enzyme_Commission_number.
The Present
Fast forward 50 years, and the Enzyme Commission (EC) is
still going strong. The importance and usefulness of the EC numbers has only increased
with time. With the explosion in sequencing volume, having an accurate genome annotation
has become critical, and EC numbers provide a well-defined, non-ambiguous
method for annotation of enzyme function. Software packages such as Pathway
Tools make the most out of this information, assigning the appropriate
reactions to the annotated genes based on their EC numbers when building
metabolic networks for newly-sequenced genomes. The content of the enzyme list,
which used to be published in books, is made available through two online
databases that are updated several times a year. A searchable MySQL version of
the database, including downloadble data in multiple formats, is available at the
ExplorEnz database at http://enzyme-database.org.
More than 5600 enzymes are currently classified, and hundreds are added each
year.
Who is the EC?
The Enzyme Commission is now part of the IUPAC-IUBMB Joint
Commission on Biochemical Nomenclature (JCBN).
It consists of a small number of experts who volunteer their time to the
project. Active members (listed alphabetically) include K. Axelsen
(Switzerland), R. Cammack (UK), R. Caspi (USA), M. Kotera (Japan), A. McDonald
(Ireland), G.P. Moss (UK), D. Schomburg (Germany), I. Schomburg (Germany), and
K.F. Tipton (Ireland). The commission members are using an online curation
system that was developed by A. McDonald, called ExplorEnz. Members of the
committee continue to classify new enzymes, modify existing entries as new
information becomes available, and extend or modify the classification rules to
accommodate new challenges.
If you would like to request a new EC entry for an enzyme
that hasn’t been classified yet, or submit an error or update report about an
existing entry, submission forms are available at http://enzyme-database.org/forms.php.
Since MetaCyc curator R. Caspi is a member of the EC, you are also welcome to
send EC-related questions or comments to biocyc-support@AI.SRI.COM.
Additional Information
- Dixon, M. and Webb, E.C. (1958), Enzymes. Longmans Green, London, pp. 183–227.
- Tipton, K. and Boyce, S. (2000) History of the enzyme nomenclature system. Bioinformatics, 16, 34-40.
- McDonald, A.G., Boyce, S. and Tipton, K.F. (2009) ExplorEnz: the primary source of the IUBMB enzyme list. Nucleic Acids Res, 37, D593-597.
- McDonald, A.G. and Tipton, K.F. (2014) Fifty-five years of enzyme classification: advances and difficulties. Febs J, 281, 583-592.
Thanks for the lovely post. Can someone comment on the pros and cons of ExplorEnz vs. the KEGG database? Is the basic difference that ExplorEnz is downloadable?
ReplyDeleteExplorEnz is a database centred on enzymes whereas KEGG is the Kyoto Encyclopedia of genes a genomes, so it includes informataion referring to whole genomes, annotations, as well as pathways pathways. I think KEGG is something more similar to the MetaCyc/BioCyc than to ExplorEnz. Hope it helps :D
ReplyDeleteCheers,
Miguel
I would say that ExpolrEnz is even more specific. It is not exactly an enzyme database (unlike Brenda, for example), because you can't look up a specific enzyme from, say, E. coli, in it. It is a database of types of enzymes, as represented by the EC classification. Because the EC classifies the enzymes based on the reactions they catalyze, ExplorEnz also includes reactions, but it does not include the compound structures or composition.
ReplyDeleteKEGG and MetaCyc/BioCyc are much more comprehensive, including information about genes, reactions, metabolites, and pathways, and even offer metabolic reconstructions for specific organisms. Both incorporate the data from ExplorEnz, but only ExplorEnz is the official database of the Enzyme Commission.
Thanks!!!
ReplyDeleteFor a EC number to be assigned to an enzyme is it important to validate the reaction experimentally ? Many Enzymes in genomes which are computationally annotated have EC numbers assigned to them
ReplyDeleteThe original EC number definition, as created by the Enzyme Commission, is based on biochemical information. However, once the EC number is established, other facilities (such as sequencing facilities, UniProt, BioCyc or KEGG) apply the EC number to putative orthologous enzymes that have not been characterized biochemically. So no, it is not required to test an enzyme biochemically before assigning it an EC number. Of course, as in all computational assignments, errors are not unusual.
ReplyDelete