Enzyme Nomenclature News
[Prepared by Ida Schomburg]
Besides the eukaryotes and the prokaryotes, the archaea represent the third domain of life. They are unicellular and similar to bacteria in shape and size, but their metabolism resembles eukaryotic behaviour in many aspects, notably the enzymes involved in archaeal DNA replication. Archaea are ubiquitous and have been found in practically all environments. Species living under extreme conditions such as hot, highly saline, alkaline or acidic waters, or under high pressure in the deep sea, were the first to be discovered. These "extremophiles" developed special strategies to maintain the stability of their cellular structure and to thrive despite limited nutrient supply, making for unique and interesting enzymes. In this short communication we will list of a few of the specialized enzymes found in archaea.
For surviving under harsh conditions the cellular structures must be highly stable. Archaeal membranes achieve that by containing archaetidylserine (2,3-bis-(O-phytanyl)-sn-glycero-1-phospho-L-serine), which is based on glycerol ether components instead of glycerol fatty acid esters. The enzymes involved in the biosynthesis of archaeal lipids have been newly classified and are shown in the diagram for archaetidylserine biosynthesis.
Polyamines are required to maintain the stability of double-stranded DNA. Where eukaryotes and prokaryotes produce linear spermine and spermidine, archaea synthesize branched-chain and long-chain polyamines, such as N4-bis(aminopropyl)spermidine or caldopentamine, which confer a higher stability. The enzymes involved in their synthesis are classified as EC 184.108.40.206 and EC 220.127.116.11.
During their long evolution archaea developed strategies for taking up nutrients very efficiently. The substrate specificity of archaeal enzymes is often less strict than that of their bacterial counterparts. For example, two new enzymes of the archaeal Entner-Doudoroff pathway have been described, one being able to dehydrogenate either glucose or galactose (EC 18.104.22.1680) and the other, with even less specificity, is able to dehydrogenate a broad range of aldoses (EC 22.214.171.1249). In addition, archaea do not follow the classical route of the Entner-Doudoroff pathway, and instead use semi- or non-phosphorylative variants. Three enzymes that participate in these pathways have been newly classified: EC 126.96.36.199, EC 188.8.131.52 and EC 184.108.40.206.
Fatty acid desaturases
[Prepared by Ron Caspi]
Fatty acid desaturases are enzymes that convert a single bond between two carbon atoms in a fatty acyl chain to a double bond. A common property for all known desaturases is their requirement for molecular oxygen and a source of electrons.
The classification of desaturase enzymes is complicated by the fact that they can be classified by several criteria. First, they differ in their substrate preferences. Free fatty acids are very rare in the cell, and fatty acids are usually found bound to either coenzyme A, acyl-carrier proteins, or as part of a glycerolipid. Desaturase enzymes are specific for one of these forms, and often are also specific for a substrate of a particular size or size range. Next, the enzymes differ in their electron donor. Most fatty acid desaturases utilize electrons provided by either ferredoxin or cytochrome b5, although some exceptions do occur. In many of the cytochrome b5-dependent enzymes gene fusion has resulted in a cytochrome b5 domain integrated into the enzyme. The enzymes can also be classified based on the position of the double bond that they introduce - some introduce it at a certain distance from the carboxylic end of the fatty acid, others determine the position based on its distance from the methyl end of the substrate, and yet others introduce the new double bond only at a particular position relative to an existing double bond. Finally, desaturases differ in the type of bond they introduce — some introduce a cis (Z) bond, others introduce a trans (E) bond, yet some introduce a mixture of both types.
Owing to the rapid increase in the number of different desaturases that were discovered in bacteria, algae, plants, fungi, and animals, the existing classifications in the Enzyme List became unsatisfactory. We have recently reviewed the existing literature and updated the list, resulting in a major revision of the fatty acid desaturase entries. We have revised most of our existing entries to eliminate ambiguity and added a large number of new entries, achieving close to full coverage of current knowledge in the field.
We tried to address all of the considerations described above. For example, EC 220.127.116.11 stands for sn-2 acyl-lipid ω-3 desaturase (ferredoxin), an enzyme that acts on acyl chains attached to position sn-2 of glycerolipids, introduces a double bond three carbons away from the methyl end of the chain, and accepts electrons from ferredoxin. Naturally, additional information can be gathered by looking at the reaction equations and reading the comment and references.
To see the entries, search the list for the name ‘‘desaturase’’ and scroll down to the entries that start with 1.14.19.