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International Journal of Molecular... Feb 2024The uridine diphosphate glycosyltransferase (UGT) superfamily plays a key role in the metabolism of xenobiotics and metabolic wastes, which is essential for detoxifying... (Review)
Review
The uridine diphosphate glycosyltransferase (UGT) superfamily plays a key role in the metabolism of xenobiotics and metabolic wastes, which is essential for detoxifying those species. Over the last several decades, a huge effort has been put into studying human and mammalian UGT homologs, but family members in other organisms have been explored much less. Potentially, other UGT homologs can have desirable substrate specificity and biological activities that can be harnessed for detoxification in various medical settings. In this review article, we take a plant UGT homology, UGT71G1, and compare its structural and biochemical properties with the human homologs. These comparisons suggest that even though mammalian and plant UGTs are functional in different environments, they may support similar biochemical activities based on their protein structure and function. The known biological functions of these homologs are discussed so as to provide insights into the use of UGT homologs from other organisms for addressing human diseases related to UGTs.
Topics: Animals; Humans; Glycosyltransferases; Uridine Diphosphate; Plants; Phylogeny; Mammals
PubMed: 38474028
DOI: 10.3390/ijms25052782 -
ELife Nov 2023As a major class of biomolecules, carbohydrates play indispensable roles in various biological processes. However, it remains largely unknown how carbohydrates directly...
As a major class of biomolecules, carbohydrates play indispensable roles in various biological processes. However, it remains largely unknown how carbohydrates directly modulate important drug targets, such as G-protein coupled receptors (GPCRs). Here, we employed P2Y purinoceptor 14 (P2Y14), a drug target for inflammation and immune responses, to uncover the sugar nucleotide activation of GPCRs. Integrating molecular dynamics simulation with functional study, we identified the uridine diphosphate (UDP)-sugar-binding site on P2Y14, and revealed that a UDP-glucose might activate the receptor by bridging the transmembrane (TM) helices 2 and 7. Between TM2 and TM7 of P2Y14, a conserved salt bridging chain (K-D-K-E [KDKE]) was identified to distinguish different UDP-sugars, including UDP-glucose, UDP-galactose, UDP-glucuronic acid, and UDP--acetylglucosamine. We identified the KDKE chain as a conserved functional motif of sugar binding for both P2Y14 and P2Y purinoceptor 12 (P2Y12), and then designed three sugar nucleotides as agonists of P2Y12. These results not only expand our understanding for activation of purinergic receptors but also provide insights for the carbohydrate drug development for GPCRs.
Topics: Receptors, Purinergic; Nucleotides; Uridine Diphosphate Glucose; Sugars; Receptors, Purinergic P2Y
PubMed: 37955640
DOI: 10.7554/eLife.85449 -
Biomolecules Apr 2022Cytidine-5'-triphosphate (CTP) synthase (CTPS) is the class I glutamine-dependent amidotransferase (GAT) that catalyzes the last step in the de novo biosynthesis of CTP.... (Review)
Review
Cytidine-5'-triphosphate (CTP) synthase (CTPS) is the class I glutamine-dependent amidotransferase (GAT) that catalyzes the last step in the de novo biosynthesis of CTP. Glutamine hydrolysis is catalyzed in the GAT domain and the liberated ammonia is transferred via an intramolecular tunnel to the synthase domain where the ATP-dependent amination of UTP occurs to form CTP. CTPS is unique among the glutamine-dependent amidotransferases, requiring an allosteric effector (GTP) to activate the GAT domain for efficient glutamine hydrolysis. Recently, the first cryo-electron microscopy structure of CTPS was solved with bound ATP, UTP, and, notably, GTP, as well as the covalent adduct with 6-diazo-5-oxo-l-norleucine. This structural information, along with the numerous site-directed mutagenesis, kinetics, and structural studies conducted over the past 50 years, provide more detailed insights into the elaborate conformational changes that accompany GTP binding at the GAT domain and their contribution to catalysis. Interactions between GTP and the L2 loop, the L4 loop from an adjacent protomer, the L11 lid, and the L13 loop (or unique flexible "wing" region), induce conformational changes that promote the hydrolysis of glutamine at the GAT domain; however, direct experimental evidence on the specific mechanism by which these conformational changes facilitate catalysis at the GAT domain is still lacking. Significantly, the conformational changes induced by GTP binding also affect the assembly and maintenance of the NH tunnel. Hence, in addition to promoting glutamine hydrolysis, the allosteric effector plays an important role in coordinating the reactions catalyzed by the GAT and synthase domains of CTPS.
Topics: Adenosine Triphosphate; Allosteric Regulation; Carbon-Nitrogen Ligases; Cryoelectron Microscopy; Cytidine Triphosphate; Glutaminase; Glutamine; Guanosine Triphosphate; Nitric Oxide Synthase; Uridine Triphosphate
PubMed: 35625575
DOI: 10.3390/biom12050647 -
International Journal of Molecular... Nov 2022The activity of phosphate groups of phosphoethanolamine and pyrimidine nucleotides (thymidine 5-monophosphate, cytidine 5-monophosphate and uridine 5'monophosphate) in...
The activity of phosphate groups of phosphoethanolamine and pyrimidine nucleotides (thymidine 5-monophosphate, cytidine 5-monophosphate and uridine 5'monophosphate) in the process of complexation metal ions in aqueous solution was studied. Using the potentiometric method with computer calculation of the data and spectroscopic methods such as UV-Vis, EPR, C and P NMR as well as FT-IR, the overall stability constants of the complexes as well as coordination modes were obtained. At lower pH, copper(II) ions are complexed only by phosphate groups, whereas the endocyclic nitrogen atom of nucleotides has been identified as a negative center interacting with the -NH groups of phosphoethanolamine.
Topics: Pyrimidine Nucleotides; Copper; Phosphates; Spectroscopy, Fourier Transform Infrared; Ions; Cytidine Monophosphate
PubMed: 36430195
DOI: 10.3390/ijms232213718 -
Molecules (Basel, Switzerland) Jun 2022TiCT MXene has attracted considerable interest as a new emerging two-dimensional material for environmental remediation due to its high adsorption capacity. However, its...
TiCT MXene has attracted considerable interest as a new emerging two-dimensional material for environmental remediation due to its high adsorption capacity. However, its use is greatly limited by its poor mechanical properties, low processability and recyclability, and the low dispersity of such powder materials. In this work, a porous adsorbent (C-CMP) containing cellulose nanocrystals (CNC), TiCT MXene and polyvinyl alcohol (PVA) was prepared by a simple and environmentally-friendly foaming method. Glutaraldehyde was used as crosslinker to improve the mechanical properties and boost the adsorption efficiency of methylene blue (MB) molecules. Fourier transform infrared (FT-IR), elemental analysis (EDX) and thermogravimetric analysis (TGA) further confirmed that the preparation of the C-CMP foam and cross-linking reaction were successful. Scanning electron microscope (SEM) indicated that the macropores were distributed homogeneously. The adsorption experiment showed that maximum adsorption capacity of MB can reach 239.92 mg·g which was much higher than anionic dye (methyl orange, 45.25 mg·g). The adsorption behavior fitted well with the Langmuir isotherm and pseudo-second-order kinetic models. Thermodynamic analysis indicated that the adsorption process was spontaneous and endothermic. Based on FT-IR, EDX and X-ray photoelectron spectroscopy (XPS) analysis, the adsorption mechanism between C-CMP and MB molecules was attributed to electrostatic interaction.
Topics: Adsorption; Cellulose; Cytidine Monophosphate; Kinetics; Methylene Blue; Spectroscopy, Fourier Transform Infrared; Water Pollutants, Chemical; Water Purification
PubMed: 35807488
DOI: 10.3390/molecules27134243 -
Archives of Biochemistry and Biophysics Oct 2017Thymidylate is synthesized de novo in all living organisms for replication of genomes. The chemical transformation is reductive methylation of deoxyuridylate at C5 to... (Review)
Review
Thymidylate is synthesized de novo in all living organisms for replication of genomes. The chemical transformation is reductive methylation of deoxyuridylate at C5 to form deoxythymidylate. All eukaryotes including humans complete this well-understood transformation with thymidylate synthase utilizing 6R-N-N-methylene-5,6,7,8-tetrahydrofolate as both a source of methylene and a reducing hydride. In 2002, flavin-dependent thymidylate synthase was discovered as a new pathway for de novo thymidylate synthesis. The flavin-dependent catalytic mechanism is different than thymidylate synthase because it requires flavin as a reducing agent and methylene transporter. This catalytic mechanism is not well-understood, but since it is known to be very different from thymidylate synthase, there is potential for mechanism-based inhibitors that can selectively inhibit the flavin-dependent enzyme to target many human pathogens with low host toxicity.
Topics: Flavins; Flavoproteins; Methylation; Tetrahydrofolates; Thymidine Monophosphate; Thymidylate Synthase
PubMed: 28821425
DOI: 10.1016/j.abb.2017.08.011 -
Cells Jan 2022The etiology of dry mouth conditions is multi-faceted. Patients radiated after head and neck cancer (HNC) and those with primary Sjögren's syndrome (pSS) share many of...
The etiology of dry mouth conditions is multi-faceted. Patients radiated after head and neck cancer (HNC) and those with primary Sjögren's syndrome (pSS) share many of the same symptoms despite different causes. With the aim of better understanding the pathophysiology and biochemical processes behind dry mouth with different etiologies, we investigated the metabolic profile of 10 HNC patients, 9 pSS patients and 10 healthy controls using high-performance liquid chromatography-high resolution mass spectrometry (HPLC-MS) metabolomics. Principal component analysis (PCA) revealed different metabolic profiles when comparing all subjects included in the study. Both patient groups showed higher ratios of several pyrimidine nucleotides and nucleosides when compared to controls. This finding may indicate that purinergic signaling plays a role in dry mouth conditions. Moreover, significantly increased levels of DL-3-aminoisobutyric acid were found in HNC patients when compared to controls, and a similar tendency was observed in the pSS patients. Furthermore, a dysregulation in amino acid metabolism was observed in both patient groups. In conclusion, metabolomics analysis showed separate metabolic profiles for HNC and pSS patients as compared to controls that could be useful in diagnostics and for elucidating the different pathophysiologies. The demonstrated dysregulation of pyrimidine nucleotides and levels of metabolites derived from amino acids in the patient groups should be studied further.
Topics: Head and Neck Neoplasms; Humans; Metabolomics; Pyrimidine Nucleotides; Saliva; Sjogren's Syndrome; Xerostomia
PubMed: 35159133
DOI: 10.3390/cells11030323 -
Proceedings of the National Academy of... Apr 2018We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers...
We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers and (6-4) pyrimidine-pyrimidone photoproducts in the genome. We find that these photoproducts are removed from the genome primarily by incisions 13-18 nucleotides 5' and 6-7 nucleotides 3' to the UV damage that generate 21- to 27-nt-long excision products. Analyses of the excision repair kinetics both in single genes and at the genome-wide level reveal strong transcription-coupled repair of the transcribed strand at early time points followed by predominantly nontranscribed strand repair at later stages. We have also characterized the excision repair level as a function of the transcription level. The availability of high-resolution and dynamic repair maps should aid in future repair and mutagenesis studies in this model organism.
Topics: DNA Damage; DNA Repair; DNA, Fungal; Genome, Fungal; Pyrimidine Dimers; Saccharomyces cerevisiae; Transcription, Genetic; Ultraviolet Rays
PubMed: 29581276
DOI: 10.1073/pnas.1801687115 -
Biochemistry Feb 2020Viperin is a radical -adenosylmethionine (SAM) enzyme that inhibits viral replication by converting cytidine triphosphate (CTP) into 3'-deoxy-3',4'-didehydro-CTP and by...
Viperin is a radical -adenosylmethionine (SAM) enzyme that inhibits viral replication by converting cytidine triphosphate (CTP) into 3'-deoxy-3',4'-didehydro-CTP and by additional undefined mechanisms operating through its N- and C-terminal domains. Here, we describe crystal structures of viperin bound to a SAM analogue and CTP or uridine triphosphate (UTP) and report kinetic parameters for viperin-catalyzed reactions with CTP or UTP as substrates. Viperin orients the C4' hydrogen atom of CTP and UTP similarly for abstraction by a 5'-deoxyadenosyl radical, but the uracil moiety introduces unfavorable interactions that prevent tight binding of UTP. Consistently, is similar for CTP and UTP whereas the for UTP is much greater. The structures also show that nucleotide binding results in ordering of the C-terminal tail and reveal that this region contains a P-loop that binds the γ-phosphate of the bound nucleotide. Collectively, the results explain the selectivity for CTP and reveal a structural role for the C-terminal tail in binding CTP and UTP.
Topics: Animals; Crystallography, X-Ray; Cytidine Triphosphate; Kinetics; Mice; Models, Molecular; Molecular Structure; Mutation; Proteins; S-Adenosylhomocysteine; Substrate Specificity; Uridine Triphosphate
PubMed: 31917549
DOI: 10.1021/acs.biochem.9b00741 -
Chemical & Pharmaceutical Bulletin 2016In the endoplasmic reticulum (ER), uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferase 1 (UGGT1) recognizes misfolded glycoproteins and transfers a glucose... (Review)
Review
In the endoplasmic reticulum (ER), uridine 5'-diphosphate-glucose: glycoprotein glucosyltransferase 1 (UGGT1) recognizes misfolded glycoproteins and transfers a glucose residue to the specific non-reducing end of high-mannose-type glycans. However, precise molecular mechanism by which UGGT1 senses the folding has not been understood clearly. To address this issue, various model substrates for UGGT1 have been prepared using biological approaches. Recently, we introduced chemical approaches using synthetic glycan probes that were designed for studying N-glycan processing in the ER and Golgi apparatus. Our approach can outfit the homogeneous and functionalized glycan probes. In this review, recent results on functional analysis of UGGT1 are summarized.
Topics: Endoplasmic Reticulum; Glucosyltransferases; Humans; Uridine Diphosphate Glucose
PubMed: 27373624
DOI: 10.1248/cpb.c16-00209