Acofactor is a non-proteinchemical compound ormetallic ion that is required for anenzyme's role as acatalyst (a catalyst is a substance that increases the rate of achemical reaction). Cofactors can be considered "helper molecules" that assist inbiochemical transformations. The rates at which these happen are characterized in an area of study calledenzyme kinetics. Cofactors typically differ fromligands in that they often derive their function by remaining bound.
Cofactors can be classified into two types:inorganic ions and complexorganic molecules calledcoenzymes.[1] Coenzymes are mostly derived fromvitamins and other organicessential nutrients in small amounts. (Some scientists limit the use of the term "cofactor" for inorganic substances; both types are included here.[2][3])
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.[4] 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 anapoenzyme, while the complete enzyme with cofactor is called aholoenzyme.[5][page needed]
TheInternational 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.[6]
Organic cofactors are oftenvitamins or made from vitamins. Many contain thenucleotideadenosine monophosphate (AMP) as part of their structures, such asATP,coenzyme A,FAD, andNAD+. This common structure may reflect a common evolutionary origin as part ofribozymes in an ancientRNA 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.[9]
Cofactors can be divided into two major groups:organiccofactors, such asflavin orheme; andinorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+ andiron–sulfur clusters.
Organic cofactors are sometimes further divided intocoenzymes andprosthetic 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 inTrends 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 andsubstrate that is required for enzyme activity and a prosthetic group as a substance that undergoes its wholecatalytic 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.[10]
In many cases, the cofactor includes both an inorganic and organic component. One diverse set of examples is theheme proteins, which consist of aporphyrin ring coordinated toiron.[22]
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.[23]
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.[5][24][25][26] In the latter case, when it is difficult to remove without denaturing the enzyme, it can be called aprosthetic group. There is no sharp division between loosely and tightly bound cofactors.[5] Many such as NAD+ can be tightly bound in some enzymes, while it is loosely bound in others.[5] Another example isthiamine pyrophosphate (TPP), which is tightly bound intransketolase orpyruvate decarboxylase, while it is less tightly bound inpyruvate dehydrogenase.[27] Other coenzymes,flavin adenine dinucleotide (FAD),biotin, andlipoamide, for instance, are tightly bound.[28] 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., vitaminsB1,B2,B6,B12,niacin,folic acid) or as coenzymes themselves (e.g.,vitamin C). However, vitamins do have other functions in the body.[29] Many organic cofactors also contain anucleotide, such as the electron carriersNAD andFAD, andcoenzyme A, which carriesacyl 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 inmethanogens, which are restricted to this group ofarchaea.[30]
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer offunctional groups.[60] This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.[61] These group-transfer intermediates are the loosely bound organic cofactors, often calledcoenzymes.
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 thedehydrogenases that usenicotinamide adenine dinucleotide (NAD+) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates andreduce NAD+ to NADH. This reduced cofactor is then a substrate for any of thereductases in the cell that require electrons to reduce their substrates.[32]
Therefore, these cofactors are continuously recycled as part ofmetabolism. 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 thehydrolysis 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.[62] This means that each ATP molecule is recycled 1000 to 1500 times daily.
Organic cofactors, such asATP andNADH, are present in all known forms of life and form a core part ofmetabolism. Such universalconservation indicates that these molecules evolved very early in the development of living things.[63] At least some of the current set of cofactors may, therefore, have been present in thelast universal ancestor, which lived about 4 billion years ago.[64][65]
Organic cofactors may have been present even earlier in thehistory of life on Earth.[66] The nucleotideadenosine is a cofactor for many basic metabolic enzymes such as transferases. It may be a remnant of theRNA world.[67][68] Adenosine-based cofactors may have acted as adaptors that allowed enzymes and ribozymes to bind new cofactors through small modifications in existing adenosine-bindingdomains, which had originally evolved to bind a different cofactor.[9] This process of adapting a pre-evolved structure for a novel use is known asexaptation.
Changes in coenzymes. A computational method, IPRO, recently predicted mutations that experimentally switched the cofactor specificity ofCandida boidinii xylose reductase from NADPH to NADH.[72]
Evolution of enzymes without coenzymes. If enzymes require a co-enzyme, how does the coenzyme evolve? The most likely scenario is that enzymes can function initially without their coenzymes and later recruit the coenzyme, even if the catalyzed reaction may not be as efficient or as fast. Examples areAlcohol Dehydrogenase (coenzyme:NAD⁺),[73]Lactate Dehydrogenase (NAD⁺),[74]Glutathione Reductase (NADPH).[75]
The first organic cofactor to be discovered was NAD+, which was identified byArthur Harden and William Young 1906.[76] They noticed that adding boiled and filteredyeast extract greatly acceleratedalcoholic fermentation in unboiled yeast extracts. They called the unidentified factor responsible for this effect acoferment. Through a long and difficult purification from yeast extracts, this heat-stable factor was identified as anucleotide sugar phosphate byHans von Euler-Chelpin.[77] Other cofactors were identified throughout the early 20th century, with ATP being isolated in 1929 by Karl Lohmann,[78] and coenzyme A being discovered in 1945 byFritz Albert Lipmann.[79]
The functions of these molecules were at first mysterious, but, in 1936,Otto Heinrich Warburg identified the function of NAD+ in hydride transfer.[80] This discovery was followed in the early 1940s by the work ofHerman Kalckar, who established the link between the oxidation of sugars and the generation of ATP.[81] This confirmed the central role of ATP in energy transfer that had been proposed by Fritz Albert Lipmann in 1941.[82] Later, in 1949, Morris Friedkin andAlbert L. Lehninger proved that NAD+ linked metabolic pathways such as the citric acid cycle and the synthesis of ATP.[83]
In a number of enzymes, the moiety that acts as a cofactor is formed by post-translational modification of a part of the protein sequence. This often replaces the need for an external binding factor, such as a metal ion, for protein function. Potential modifications could be oxidation of aromatic residues, binding between residues, cleavage or ring-forming.[84] These alterations are distinct from otherpost-translation protein modifications, such asphosphorylation,methylation, orglycosylation in that the amino acids typically acquire new functions. This increases the functionality of the protein; unmodified amino acids are typically limited to acid-base reactions, and the alteration of resides can give the protein electrophilic sites or the ability to stabilize free radicals.[84] Examples of cofactor production includetryptophan tryptophylquinone (TTQ), derived from two tryptophan side chains,[85] and 4-methylidene-imidazole-5-one (MIO), derived from an Ala-Ser-Gly motif.[86] Characterization of protein-derived cofactors is conducted usingX-ray crystallography andmass spectroscopy; structural data is necessary because sequencing does not readily identify the altered sites.
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 ashormones that bind to and activatereceptor proteins are termed cofactors or coactivators, whereas molecules that inhibit receptor proteins are termed corepressors. One such example is the G protein-coupled receptor family of receptors, which are frequently found in sensory neurons. Ligand binding to the receptors activates the G protein, which then activates an enzyme to activate the effector.[87] In order to avoid confusion, it has been suggested that such proteins that have ligand-binding mediated activation or repression be referred to as coregulators.[88]
^abDenessiouk KA, Rantanen VV, Johnson MS (August 2001). "Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins".Proteins.44 (3):282–91.doi:10.1002/prot.1093.PMID11455601.S2CID10848692.
^Aggett PJ (August 1985). "Physiology and metabolism of essential trace elements: an outline".Clinics in Endocrinology and Metabolism.14 (3):513–43.doi:10.1016/S0300-595X(85)80005-0.PMID3905079.
^Niki I, Yokokura H, Sudo T, Kato M, Hidaka H (October 1996). "Ca2+ signaling and intracellular Ca2+ binding proteins".Journal of Biochemistry.120 (4):685–98.doi:10.1093/oxfordjournals.jbchem.a021466.PMID8947828.
^Eady RR (July 1988). "The vanadium-containing nitrogenase of Azotobacter".BioFactors.1 (2):111–6.PMID3076437.
^Warburg O, Christian W (1936). "Pyridin, the hydrogen-transferring component of the fermentation enzymes (pyridine nucleotide)".Biochemische Zeitschrift.287:E79 –E88.doi:10.1002/hlca.193601901199.
