A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's role as a catalyst. Cofactors can be considered "helper molecules" that assist in biochemical transformations. The rates at which these happen are characterized in an area of study called enzyme kinetics. Cofactors typically differ from ligands in that they often derive their function by remaining bound.
Cofactors can be classified into two types: inorganic ions and complex organic molecules called coenzymes. Coenzymes are mainly derived from vitamins and other organic essential nutrients in small amounts (some definitions limit the use of the term "cofactor" for inorganic substances; both types are included here).
Coenzymes are further divided into two types. The first is called a "prosthetic group", which consists of a coenzyme that is tightly (or even covalently and, therefore, permanently) bound to a protein. The second type of coenzymes are called "cosubstrates", and are transiently bound to the protein. Cosubstrates may be released from a protein at some point, and then rebind later. Both prosthetic groups and cosubstrates have the same function, which is to facilitate the reaction of enzymes and proteins. An inactive enzyme without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is called a holoenzyme.
The International Union of Pure and Applied Chemistry (IUPAC) defines "coenzyme" a little differently, namely as a low-molecular-weight, non-protein organic compound that is loosely attached, participating in enzymatic reactions as a dissociable carrier of chemical groups or electrons; a prosthetic group is defined as a tightly bound, nonpolypeptide unit in a protein that is regenerated in each enzymatic turnover.
Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase at the junction of glycolysis and the citric acid cycle requires five organic cofactors and one metal ion: loosely bound thiamine pyrophosphate (TPP), covalently bound lipoamide and flavin adenine dinucleotide (FAD), cosubstrates nicotinamide adenine dinucleotide (NAD+) and coenzyme A (CoA), and a metal ion (Mg2+).
Organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered to be a kind of "handle" by which the enzyme can "grasp" the coenzyme to switch it between different catalytic centers.
Classification Cofactors can be divided into two major groups: organic cofactors, such as flavin or heme; and inorganic cofactors, such as the metal ions Mg2+, Zn2+, Cu+, Mn2+ and iron–sulfur clusters.
Organic cofactors are sometimes further divided into coenzymes and prosthetic groups. The term coenzyme refers specifically to enzymes and, as such, to the functional properties of a protein. On the other hand, "prosthetic group" emphasizes the nature of the binding of a cofactor to a protein (tight or covalent) and, thus, refers to a structural property. Different sources give slightly different definitions of coenzymes, cofactors, and prosthetic groups. Some consider tightly bound organic molecules as prosthetic groups and not as coenzymes, while others define all non-protein organic molecules needed for enzyme activity as coenzymes, and classify those that are tightly bound as coenzyme prosthetic groups. These terms are often used loosely.
A 1980 letter in Trends in Biochemistry Sciences noted the confusion in the literature and the essentially arbitrary distinction made between prosthetic groups and coenzymes group and proposed the following scheme. Here, cofactors were defined as an additional substance apart from protein and substrate that is required for enzyme activity and a prosthetic group as a substance that undergoes its whole catalytic cycle attached to a single enzyme molecule. However, the author could not arrive at a single all-encompassing definition of a "coenzyme" and proposed that this term be dropped from use in the literature.
Inorganic cofactors
Metal ions
Metal ions are common cofactors. The study of these cofactors falls under the area of bioinorganic chemistry. In nutrition, the list of essential trace elements reflects their role as cofactors. In humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum. Although chromium deficiency causes impaired glucose tolerance, no human enzyme that uses this metal as a cofactor has been identified. Iodine is also an essential trace element, but this element is used as part of the structure of thyroid hormones rather than as an enzyme cofactor. Calcium is another special case, in that it is required as a component of the human diet, and it is needed for the full activity of many enzymes, such as nitric oxide synthase, protein phosphatases, and adenylate kinase, but calcium activates these enzymes in allosteric regulation, often binding to these enzymes in a complex with calmodulin. Calcium is, therefore, a cell signaling ion, and not usually considered a cofactor of the enzymes it regulates.
Other organisms require additional metals as enzyme cofactors, such as vanadium in the nitrogenase of the nitrogen-fixing bacteria of the genus Azotobacter, tungsten in the aldehyde ferredoxin oxidoreductase of the thermophilic archaean Pyrococcus furiosus, and even cadmium in the carbonic anhydrase from the marine diatom Thalassiosira weissflogii.
In many cases, the cofactor includes both an inorganic and organic component. One diverse set of examples is the heme proteins, which consist of a porphyrin ring coordinated to iron.
IonExamples of enzymes containing this ionCupric Cytochrome oxidaseFerrous or Ferric CatalaseCytochrome (via Heme)NitrogenaseHydrogenaseMagnesium Glucose 6-phosphataseHexokinase DNA polymeraseManganese ArginaseMolybdenum Nitrate reductaseNitrogenaseXanthine oxidaseNickel UreaseZinc Alcohol dehydrogenaseCarbonic anhydraseDNA polymerase
Iron–sulfur clusters
Iron–sulfur clusters are complexes of iron and sulfur atoms held within proteins by cysteinyl residues. They play both structural and functional roles, including electron transfer, redox sensing, and as structural modules.
Organic Organic cofactors are small organic molecules (typically a molecular mass less than 1000 Da) that can be either loosely or tightly bound to the enzyme and directly participate in the reaction. In the latter case, when it is difficult to remove without denaturing the enzyme, it can be called a prosthetic group. There is no sharp division between loosely and tightly bound cofactors. Many such as NAD+ can be tightly bound in some enzymes, while it is loosely bound in others. Another example is thiamine pyrophosphate (TPP), which is tightly bound in transketolase or pyruvate decarboxylase, while it is less tightly bound in pyruvate dehydrogenase. Other coenzymes, flavin adenine dinucleotide (FAD), biotin, and lipoamide, for instance, are tightly bound. Tightly bound cofactors are, in general, regenerated during the same reaction cycle, while loosely bound cofactors can be regenerated in a subsequent reaction catalyzed by a different enzyme. In the latter case, the cofactor can also be considered a substrate or cosubstrate.
Vitamins can serve as precursors to many organic cofactors (e.g., vitamins B1, B2, B6, B12, niacin, folic acid) or as coenzymes themselves (e.g., vitamin C). However, vitamins do have other functions in the body. Many organic cofactors also contain a nucleotide, such as the electron carriers NAD and FAD, and coenzyme A, which carries acyl groups. Most of these cofactors are found in a huge variety of species, and some are universal to all forms of life. An exception to this wide distribution is a group of unique cofactors that evolved in methanogens, which are restricted to this group of archaea.
Although enzyme catalyzed industrial processes are highly efficient, some of the enzymes are dependent on nicotinamide cofactors (NADH/NAD+, NADP/NAPH). Due to the high price of such cofactors, these processes would not be economically competitive. Recently, some synthetic organic compounds were identified as economically promising biomimetic counterparts of natural cofactors.
Vitamins and derivatives Cofactor / Prosthetic group Vitamin Additional component Chemical group(s) transferred DistributionThiamine pyrophosphate Thiamine (B1) pyrophosphate 2-carbon groups, α cleavage Bacteria, archaea and eukaryotes NAD+ and NADP+ Niacin (B3) ADP Electrons Bacteria, archaea and eukaryotes Pyridoxal phosphate Pyridoxine (B6) None Amino and carboxyl groups Bacteria, archaea and eukaryotes Methylcobalamin Vitamin B12 Methyl group acyl groups Bacteria, archaea and eukaryotes Cobalamine Cobalamine (B12) None hydrogen, alkyl groups Bacteria, archaea and eukaryotes Biotin Biotin (H) None CO2 Bacteria, archaea and eukaryotes Coenzyme A Pantothenic acid (B5) ADP Acetyl group and other acyl groups Bacteria, archaea and eukaryotes Tetrahydrofolic acid Folic acid (B9) Glutamate residues Methyl, formyl, methylene and formimino groups Bacteria, archaea and eukaryotesMenaquinone Vitamin K None Carbonyl group and electrons Bacteria, archaea and eukaryotesAscorbic acid Vitamin C None Electrons Bacteria, archaea and eukaryotes Flavin mononucleotide Riboflavin (B2) None Electrons Bacteria, archaea and eukaryotes Flavin adenine dinucleotide Riboflavin (B2) ADP Electrons Bacteria, archaea and eukaryotesCoenzyme F420 Riboflavin (B2) Amino acids Electrons Methanogens and some bacteria
Non-vitamins Cofactor Chemical group(s) transferred DistributionAdenosine triphosphate Phosphate group Bacteria, archaea and eukaryotesS-Adenosyl methionine Methyl group Bacteria, archaea and eukaryotesCoenzyme B Electrons Methanogens Coenzyme M Methyl group Methanogens Coenzyme Q Electrons Bacteria, archaea and eukaryotesCytidine triphosphate Diacylglycerols and lipid head groups Bacteria, archaea and eukaryotesGlutathione Electrons Some bacteria and most eukaryotesHeme Electrons Bacteria, archaea and eukaryotes Lipoamide Electrons, acyl groups Bacteria, archaea and eukaryotesMethanofuran Formyl group MethanogensMolybdopterin Oxygen atoms Bacteria, archaea and eukaryotesNucleotide sugars Monosaccharides Bacteria, archaea and eukaryotes3'-Phosphoadenosine-5'-phosphosulfate Sulfate group Bacteria, archaea and eukaryotesPyrroloquinoline quinone Electrons BacteriaTetrahydrobiopterin Oxygen atom and electrons Bacteria, archaea and eukaryotesTetrahydromethanopterin Methyl group Methanogens
Cofactors as metabolic intermediates
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are the loosely bound organic cofactors, often called coenzymes.
Each class of group-transfer reaction is carried out by a particular cofactor, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. An example of this are the dehydrogenases that use nicotinamide adenine dinucleotide (NAD+) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates and reduce NAD+ to NADH. This reduced cofactor is then a substrate for any of the reductases in the cell that require electrons to reduce their substrates.