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The succinate dehydrogenase complex showing several cofactors, including flavin, iron-sulfur centers, and heme.
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations.
Cofactors can be classified depending on how tightly they bind to an enzyme, with loosely bound cofactors termed coenzymes and tightly bound cofactors termed prosthetic groups. Some sources also limit the use of the term "cofactor" to inorganic substances.[1][2] An inactive enzyme, without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is the holoenzyme.[3]
Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase[4] 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), and the cosubstrates nicotinamide adenine dinucleotide (NAD+) and coenzyme A (CoA), and a metal ion (Mg2+).
Organic cofactors are often vitamins or are 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 a kind of "handle" by which the enzyme can "grasp" the coenzyme to switch it between different catalytic centers.[5]
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Classification [edit]
Cofactors can be divided into two broad groups: organic cofactors, such as flavin or heme, and inorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+, or 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. It should be noted that these terms are often used loosely.
A 1979 letter in Trends in Biochemical Sciences noted the confusion in the literature and the essentially arbitrary distinction made between prosthetic groups and coenzymes 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.[6]
Inorganic [edit]
Metal ions [edit]
Further information: Metalloproteins
Metal ions are common cofactors.[7] 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.[8] Although chromium deficiency causes impaired glucose tolerance, no human enzyme that uses this metal as a cofactor has been identified.[9][10] 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.[11] 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.[12] Calcium is, therefore, a cell signaling molecule, and not usually considered a cofactor of the enzymes it regulates.[13]
Other organisms require additional metals as enzyme cofactors, such as vanadium in the nitrogenase of the nitrogen-fixing bacteria of the genus Azotobacter,[14] tungsten in the aldehyde ferredoxin oxidoreductase of the thermophilic archaean Pyrococcus furiosus,[15] and even cadmium in the carbonic anhydrase from the marine diatom Thalassiosira weissflogii.[16][17]
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.
| Ion | Examples of enzymes containing this ion |
|---|---|
| Cupric | Cytochrome oxidase |
| Ferrous or Ferric | Catalase Cytochrome (via Heme) |
| Magnesium | Glucose 6-phosphatase Hexokinase |
| Manganese | Arginase |
| Molybdenum | Nitrate reductase Nitrogenase |
| Nickel | Urease |
| Zinc | Alcohol dehydrogenase Carbonic anhydrase |
A simple [Fe2S2] cluster containing two iron atoms and two sulfur atoms, coordinated by four protein cysteine residues.
Iron-sulfur clusters [edit]
Further information: Iron-sulfur protein
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.[18]
Organic [edit]
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.[3][19][20][21] In the latter case, when it is difficult to remove without denaturing the enzyme, it can be called a prosthetic group. It is important to emphasize that there is no sharp division between loosely and tightly bound cofactors.[3] Indeed, many such as NAD+ can be tightly bound in some enzymes, while it is loosely bound in others.[3] 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 covalently 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.[22] 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.[23]
Vitamins and derivatives [edit]
| Cofactor | Vitamin | Additional component | Chemical group(s) transferred | Distribution |
| Thiamine pyrophosphate [24] | Thiamine (B1) | None | 2-carbon groups, α cleavage | Bacteria, archaea and eukaryotes |
| NAD+ and NADP+ [25] | Niacin (B3) | ADP | Electrons | Bacteria, archaea and eukaryotes |
| Pyridoxal phosphate [26] | Pyridoxine (B6) | None | Amino and carboxyl groups | Bacteria, archaea and eukaryotes |
| Lipoamide [3] | Lipoic acid | None | electrons, acyl groups | Bacteria, archaea and eukaryotes |
| Methylcobalamin [27] | Vitamin B12 | Methyl group | acyl groups | Bacteria, archaea and eukaryotes |
| Cobalamine [3] | Cobalamine (B12) | None | hydrogen, alkyl groups | Bacteria, archaea and eukaryotes |
| Biotin [28] | Biotin (H) | None | CO2 | Bacteria, archaea and eukaryotes |
| Coenzyme A [29] | Pantothenic acid (B5) | ADP | Acetyl group and other acyl groups | Bacteria, archaea and eukaryotes |
| Tetrahydrofolic acid [30] | Folic acid (B9) | Glutamate residues | Methyl, formyl, methylene and formimino groups | Bacteria, archaea and eukaryotes |
| Menaquinone [31] | Vitamin K | None | Carbonyl group and electrons | Bacteria, archaea and eukaryotes |
| Ascorbic acid [32] | Vitamin C | None | Electrons | Bacteria, archaea and eukaryotes |
| Flavin mononucleotide [33] | Riboflavin (B2) | None | Electrons | Bacteria, archaea and eukaryotes |
| Flavin adenine dinucleotide [33] | Riboflavin (B2) | None | Electrons | Bacteria, archaea and eukaryotes |
| Coenzyme F420 [34] | Riboflavin (B2) | Amino acids | Electrons | Methanogens and some bacteria |
Non-vitamins [edit]
| Cofactor | Chemical group(s) transferred | Distribution |
| Adenosine triphosphate [35] | Phosphate group | Bacteria, archaea and eukaryotes |
| S-Adenosyl methionine [36] | Methyl group | Bacteria, archaea and eukaryotes |
| Coenzyme B [37] | Electrons | Methanogens |
| Coenzyme M [38][39] | Methyl group | Methanogens |
| Coenzyme Q [40] | Electrons | Bacteria, archaea and eukaryotes |
| Cytidine triphosphate [41] | Diacylglycerols and lipid head groups | Bacteria, archaea and eukaryotes |
| Glutathione [42][43] | Electrons | Some bacteria and most eukaryotes |
| Heme [44] | Electrons | Bacteria, archaea and eukaryotes |
| Methanofuran [45] | Formyl group | Methanogens |
| Molybdopterin [46][47] | Oxygen atoms | Bacteria, archaea and eukaryotes |
| Nucleotide sugars [48] | Monosaccharides | Bacteria, archaea and eukaryotes |
| 3'-Phosphoadenosine-5'-phosphosulfate [49] | Sulfate group | Bacteria, archaea and eukaryotes |
| Pyrroloquinoline quinone [50] | Electrons | Bacteria |
| Tetrahydrobiopterin [51] | Oxygen atom and electrons | Bacteria, archaea and eukaryotes |
| Tetrahydromethanopterin [52] | Methyl group | Methanogens |
Cofactors as metabolic intermediates [edit]
The redox reactions of nicotinamide adenine dinucleotide.
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.[53] This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.[54] 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.[25]
Therefore, these cofactors are continuously recycled as part of metabolism. As an example, the total quantity of ATP in the human body is about 0.1 mole. This ATP is constantly being broken down into ADP, and then converted back into ATP. Thus, at any given time, the total amount of ATP + ADP remains fairly constant. The energy used by human cells requires the hydrolysis of 100 to 150 moles of ATP daily, which is around 50 to 75 kg. In typical situations, humans use up their body weight of ATP over the course of the day.[55] This means that each ATP molecule is recycled 1000 to 1500 times daily.
Evolution [edit]
Further information: Abiogenesis
Organic cofactors, such as ATP and NADH, are present in all known forms of life and form a core part of metabolism. Such universal conservation indicates that these molecules evolved very early in the development of living things.[56] At least some of the current set of cofactors may, therefore, have been present in the last universal ancestor, which lived about 4 billion years ago.[57][58]
Organic cofactors may have been present even earlier in the history of life on Earth.[59] It is interesting to note that the nucleotide adenosine is present in cofactors that catalyse many basic metabolic reactions such as methyl, acyl, and phosphoryl group transfer, as well as redox reactions. This ubiquitous chemical scaffold has, therefore, been proposed to be a remnant of the RNA world, with early ribozymes evolving to bind a restricted set of nucleotides and related compounds.[60][61] Adenosine-based cofactors are thought to have acted as interchangeable adaptors that allowed enzymes and ribozymes to bind new cofactors through small modifications in existing adenosine-binding domains, which had originally evolved to bind a different cofactor.[5] This process of adapting a pre-evolved structure for a novel use is referred to as exaptation.
A computational method, IPRO, recently predicted mutations that experimentally switched the cofactor specificity of Candida boidinii xylose reductase from NADPH to NADH. Details on how to download the software implemented in Python and experimental testing of predictions are outlined in the following paper.[62]
History [edit]
Further information: History of biochemistry
The first organic cofactor to be discovered was NAD+, which was identified by Arthur Harden and William Youndin 1906.[63] They noticed that adding boiled and filtered yeast extract greatly accelerated alcoholic fermentation in unboiled yeast extracts. They called the unidentified factor responsible for this effect a coferment. Through a long and difficult purification from yeast extracts, this heat-stable factor was identified as a nucleotide sugar phosphate by Hans von Euler-Chelpin.[64] Other cofactors were identified throughout the early 20th century, with ATP being isolated in 1929 by Karl Lohmann,[65] and coenzyme A being discovered in 1945 by Fritz Albert Lipmann.[66]
The functions of these molecules were at first mysterious, but, in 1936, Otto Heinrich Warburg identified the function of NAD+ in hydride transfer.[67] This discovery was followed in the early 1940s by the work of Herman Kalckar, who established the link between the oxidation of sugars and the generation of ATP.[68] This confirmed the central role of ATP in energy transfer that had been proposed by Fritz Albert Lipmann in 1941.[69] Later, in 1949, Morris Friedkin and Albert L. Lehninger proved that NAD+ linked metabolic pathways such as the citric acid cycle and the synthesis of ATP.[70]
Non-enzymatic cofactors [edit]
The term is used in other areas of biology to refer more broadly to non-protein (or even protein) molecules that either activate, inhibit, or are required for the protein to function. For example, ligands such as hormones that bind to and activate receptor proteins are termed cofactors or coactivators, whereas molecules that inhibit receptor proteins are termed corepressors.
See also [edit]
- Enzyme catalysis
- Inorganic chemistry
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Further reading [edit]
- Bugg, Tim (1997). An introduction to enzyme and coenzyme chemistry. Oxford: Blackwell Science. ISBN 0-86542-793-3.
External links [edit]
- Cofactors lecture (Powerpoint file)
- Cofactor at eMedicine Dictionary
- Enzyme cofactors at the US National Library of Medicine Medical Subject Headings (MeSH)
- The CoFactor Database
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- 1. ビリルビン過剰産生によるジルベール症候群および高非抱合型ビリルビン血症gilbert syndrome and unconjugated hyperbilirubinemia due to bilirubin overproduction [show details]…within adipocytes, decreased conjugation due to depletion of UDP-glycuronic acid (which serves as a cosubstrate in glucuronidation), and enhanced cycling of bilirubin by the enterohepatic circulation . Intercurrent…
English Journal
- Post-translational regulation by structural changes of 4-dihydromethyltrisporate dehydrogenase, a key enzyme in sexual and parasitic communication mediated by the trisporic acid pheromone system, of the fungal fusion parasite Parasitella parasitica.
- Ellenberger S1, Burmester A2, Schuster S3, Wöstemeyer J2.
- Journal of theoretical biology.J Theor Biol.2017 Jan 21;413:50-57. doi: 10.1016/j.jtbi.2016.11.006. Epub 2016 Nov 15.
- Sexual communication between complementary mating partners in the fungal group of zygomycetes is mediated by the trisporoid pheromone system. A key enzyme towards biosynthesis of hormonally active trisporoids is 4-dihydromethyltrisporate dehydrogenase (TSP1), an enzyme occurring in all zygomycetous
- PMID 27864097
- Biocatalytic Reduction of HMF to 2,5-Bis(hydroxymethyl)furan by HMF-Tolerant Whole Cells.
- Li YM1, Zhang XY1, Li N1, Xu P1, Lou WY1, Zong MH1.
- ChemSusChem.ChemSusChem.2017 Jan 20;10(2):372-378. doi: 10.1002/cssc.201601426. Epub 2016 Dec 14.
- Catalytic upgrading of 5-hydroxymethylfurfural (HMF), an important biobased platform chemical for high-value products, is currently of great interest. In this work, a new highly HMFtolerant yeast strain-Meyerozyma guilliermondii SC1103 was isolated, and biocatalytic reduction of HMF to 2,5-bis(hydro
- PMID 27966286
- Novel AdoMet analogues as tools for enzymatic transfer of photo-crosslinkers and capturing RNA-protein interactions.
- Muttach F, Mäsing F, Studer A, Rentmeister A1.
- Chemistry (Weinheim an der Bergstrasse, Germany).Chemistry.2017 Jan 2. doi: 10.1002/chem.201605663. [Epub ahead of print]
- Elucidation of biomolecular interactions is of utmost importance in biochemistry. Photo-crosslinking offers the possibility to precisely determine RNA-protein interactions. However, despite the inherent specificity of enzymes, approaches for site-specific introduction of photo-crosslinking moieties
- PMID 28042932
Japanese Journal
- Novel high butanol production from lactic acid and pentose by Clostridium saccharoperbutylacetonicum(BIOCHEMICAL ENGINEERING)
- Yoshida Tsuyoshi,Tashiro Yukihiro,Sonomoto Kenji
- Journal of bioscience and bioengineering 114(5), 526-530, 2012-11
- … Examination for optimum cosubstrate indicated that arabinose was superior to glucose and xylose for ABE fermentation. …
- NAID 110009553586
- 硫酸塩還元条件におけるセルロースを共存基質とした高分子リグニンの分解特性
- 高 在中,清水 芳久,池田 和弘 [他],金 錫九,松井 三郎
- 廃棄物資源循環学会論文誌 = Journal of the Japan Society of Material Cycles and Waste Management 20(3), 151-160, 2009-05-30
- 本研究は嫌気性硫酸塩還元条件における高分子リグニンの分解について調べたものである。硫酸塩還元条件で，セルロースを共存基質として与え連続運転を行い，高分子リグニンの変化を定性的，定量的に追跡した。特に，高分子リグニンの分解に伴う分解産物として水溶性低分子リグニンであるAPPL (Acid Precipitable Polymeric Lignin) や芳香族化合物に着目した。<BR>その …
- NAID 10024885544
- Microbial production of xylitol from L-arabinose by metabolically engineered Escherichia coli(MICROBIAL PHYSIOLOGY AND BIOTECHNOLOGY)
- Sakakibara Yoshikiyo,Saha Badal C.,Taylor Paul
- Journal of bioscience and bioengineering 107(5), 506-511, 2009-05
- … It was determined that utilization of glycerol as a cosubstrate significantly improved xylitol production and yield. …
- NAID 110007225854
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- A co-substrate is a co-factor that transforms an apoenzyme into a holoenzyme. However, it is not tightly bound to the protein and freely binds and releases (but is not chemically altered). This is different from a tightly bound cofactor such as ...
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