Micronutrients
Chuong Pham-Huy, Bruno Pham Huy in Food and Lifestyle in Health and Disease, 2022
In general, an enzyme cannot function alone; it must be activated by one or many small molecules called coenzymes and cofactors. Some enzymes require several coenzymes and cofactors. Coenzymes and cofactors are small organic molecules or metal ions that are used by enzymes to help catalyze reactions (89–93). In other words, coenzymes are typically organic molecules that contain functionalities not found in proteins, while cofactors are catalytically essential molecules or ions that are covalently bound to enzymes (91). The term holoenzyme refers to an active enzyme complex: an enzyme combined with a coenzyme or a cofactor. An apoenzyme is an inactive enzyme: an enzyme without an activator (coenzyme or/and cofactor). The term prosthetic group is used to refer to minerals, activated vitamins, or other nonprotein compounds that are required for full enzyme activity (89–93). The prosthetic group remains bonded for the enzyme during the reaction. In some cases, the prosthetic group is covalently bound for its apoenzyme, while in other cases it is weakly bound to the active center by numerous weak interactions (93).
Cyclic Nucleotides
Enrique Pimentel in Handbook of Growth Factors, 2017
The manyfold physiologic effects of cAMP in eukaryotic cells are mediated exclusively through activation of the cAMP-dependent protein kinase (protein kinase A or A-kinase).49-53 The kinase holoenzyme is tetrameric and exists as an inactive complex of two regulatory (R) and two catalytic (C) subunits (R2C2). The R subunit contains two cAMP-binding sites, a dimer interaction site, and an autophosphorylation site. In addition, the holoenzyme contains interaction sites between the R and C subunits. Like most protein kinases, the function of the cAMP-dependent protein kinase depends on a regulatory mechanism and the enzyme is maintained in an inactive form in the absence of cAMP. When cAMP is generated by the action of hormones, growth factors, or other stimuli, it binds with a high affinity to the R subunit, and the complex dissociates to liberate active C subunits which appear to be identical. Under normal physiological conditions, this leads to dissociation of the holoenzyme into an R2-(cAMP)4 dimer and two catalytically active free C subunits. Crystal structure analysis of the C subunit at a resolution of 2.7 Å showed that the enzyme is bilobal with a deep cleft between the lobes.54 While the smaller lobe is associated with nucleotide binding, the larger lobe is primarily involved in peptide binding and catalysis.
Regulation of Synthesis of the β & β′ Subunits of RNA Polymerase of Escherichia Coli
James F. Kane in Multifunctional Proteins: Catalytic/Structural and Regulatory, 2019
Early attempts to purify the enzyme led to the isolation of a tetramer containing two α subunits, one β subunit, and one β′ subunit with molecular weights of 44,000, 150,000, and 165,000 dal tons, respectively. This enzyme was highly active in vitro when assayed with nicked template and a mixture of Mg2+ and Mn2+ divalent cations. Enzyme activity was greatly reduced when nicked template was replaced by intact DNA. High activity could be restored in the presence of the 70 kilodalton σ factor, which is now known to be required for correct promoter recognition. This factor dissociates shortly after initiation of transcription, so it is hardly surprising that it was lost in early purification procedures in which the assays for activity were not designed to score for correct initiation. Another small protein factor called co (not to be confused with the Type I topoisomerase of E. coli also called co) co-purifies with the so-called holoenzyme, but no functional activity has been demonstrated for this subunit. Other factors have been described which are believed to be required for the initiation or termination of transcription of certain gene products. The current description of the holoenzyme then is that of a pentamer containing σ, 2α, 1 β, and 1 β′ but not necessarily excluding other more or less firmly bound proteins which may be required in some or all transcriptional events.
Synthesis of substituted 15β-alkoxy estrone derivatives and their cofactor-dependent inhibitory effect on 17β-HSD1
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2019
Bianka Edina Herman, Anita Kiss, János Wölfling, Erzsébet Mernyák, Mihály Szécsi, Gyula Schneider
Cofactor-dependent affinities of some of the investigated compounds indicate that binding capabilities of the binding hole may be different depending on the nature of cofactor the enzyme complexed with. The binding hole suitable to accommodate C15 side chains is known to be formed by amino acids Leu96, Met193, Gly198, Tyr218, Leu219, and Ser22212. Residues Met193 and Gly198 are also constituents of the disordered loop (amino acids 189–200) which adopt a specific conformation following cofactor binding25,27. The presence or absence of 2′-phosphate in the cofactors causes differences in the structure of the holoenzymes. Furthermore, the area of the substrate binding site may also be affected in a different way in these complexes25,27,31. We may also assume that binding of NADPH or NADH modifies the conformation of the loop of residues 189–200 differently. Joint residues Met193 and Gly198 of the two structural elements transmit this difference from the loop to the binding hole, and these processes induce different positioning and binding capabilities of the binding hole in the holoenzyme variants. Hosting certain C15 side chains, therefore, might be, therefore, favoured or unfavoured in the binding hole altered differently upon binding of phosphorylated or unphosphorylated cofactors.
Therapeutic targets for altering mitochondrial dysfunction associated with diabetic retinopathy
Published in Expert Opinion on Therapeutic Targets, 2018
Renu A. Kowluru, Manish Mishra
The Nox family of enzymes is the main source of cytosolic ROS production and among these, Nox2 plays an active role in retinal ROS generation in diabetes. Nox2 is a highly regulated multi-protein membrane-associated enzyme which catalyzes the one-electron reduction of oxygen to superoxide anion by oxidizing cytosolic NADPH. The holoenzyme is composed of cytosolic subunits-p47phox, p67phox and a small molecular G-protein Rac1, and the membrane-bound subunits p22phox and gp91phox [26]. Rac1 activation/deactivation is mediated by specific guanine exchange factors and GTPase-activating proteins. In diabetes, Rac1–Nox2 signaling axis in the retina and its capillary cells is activated in the initial stages of diabetes to increase intracellular ROS. Inhibition of guanine exchange factor, Tiam (T-lymphoma invasion and metastasis gene), attenuates Rac1 activation and ROS generation in the retina [26]. Activation of Rac1–Nox2–ROS is an initial event, which precedes mitochondrial damage. Although in the initial stages of the disease, concomitant increase in mitochondrial DNA (mtDNA) biogenesis/repair compensates for ROS-induced mitochondrial damage [26,38], sustained hyperglycemia overwhelms the mtDNA biogenesis and repair mechanisms and initiates a vicious cycle of ROS damaging the mitochondria [2,39].
Potential therapeutic targets for Mpox: the evidence to date
Published in Expert Opinion on Therapeutic Targets, 2023
Siddappa N Byrareddy, Kalicharan Sharma, Shrikesh Sachdev, Athreya S. Reddy, Arpan Acharya, Kaylee M. Klaustermeier, Christian L Lorson, Kamal Singh
VACV DNA genome replication is conducted by a holoenzyme consisting of multiple proteins [25]. An essential component of this holoenzyme is E9, the DNA-dependent DNA polymerase belonging to B family DNA polymerases. The MPXV genome encodes F8L (OPG71) [2], also a B family DNA-dependent DNA polymerase [27], which shares ~ 98% identity with VACV E9. The first B family DNA polymerase (RB69) structure showed an overall architecture of this class of enzymes [28]. This structure showed a canonical polymerase domain consisting of the Thumb, Palm, and Fingers subdomains, as seen in the structure of the Klenow Fragment (KF) of E. coli DNA polymerase I [29]. A notable difference between these polymerases is the relative position of the 3’ − 5’ exonuclease domain, which is ~ 180° opposite to that in KF relative to the polymerase active site. Subsequent crystal structures of the RB69 polymerase showed that residues of a β-hairpin positioned in the major groove of the template-primer played a role in the partitioning of primer to the 3’ − 5’ exonuclease site upon mismatch nucleotide incorporation [28,30–32]. Indeed, a resistance mutation on topologically similar β-hairpin in poxviruses’ DNA polymerase showed the relevance of the resistance mechanism of nucleotide analogs mediated by 3’ − 5’ exonuclease function (discussed below).
Related Knowledge Centers
- Catalysis
- Chemical Reaction
- Enzyme Catalysis
- Metabolic Pathway
- Molecule
- Protein
- Metabolism
- Substrate
- Product
- Cell