-
Advances in Biological Regulation Jan 2020Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of... (Review)
Review
Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of inositol are substituted with diphosphate and monophosphate moieties. Since the discovery of PP-IPs in the early 1990s, enormous progress has been made in uncovering pleiotropic roles for these small molecules in cellular physiology. PP-IPs exert their effect on proteins in two ways - allosteric regulation by direct binding, or post-translational regulation by serine pyrophosphorylation, a modification unique to PP-IPs. Serine pyrophosphorylation is achieved by Mg-dependent, but enzyme independent transfer of a β-phosphate from a PP-IP to a pre-phosphorylated serine residue located in an acidic motif, within an intrinsically disordered protein sequence. This distinctive post-translational modification has been shown to regulate diverse cellular processes, including rRNA synthesis, glycolysis, and vesicle transport. However, our understanding of the molecular details of this phosphotransfer from pyrophospho-inositol to generate pyrophospho-serine, is still nascent. This review discusses our current knowledge of protein pyrophosphorylation, and recent advances in understanding the mechanism of this important yet overlooked post-translational modification.
Topics: Biological Transport; Diphosphates; Energy Metabolism; Eukaryotic Cells; Inositol Phosphates; Phosphorylation; Protein Processing, Post-Translational; Serine; Signal Transduction
PubMed: 31668836
DOI: 10.1016/j.jbior.2019.100662 -
Protein Science : a Publication of the... Aug 2019The Nudix hydrolase superfamily is identified by a conserved cassette of 23 amino acids, and it is characterized by its pyrophosphorylytic activity on a wide variety of...
The Nudix hydrolase superfamily is identified by a conserved cassette of 23 amino acids, and it is characterized by its pyrophosphorylytic activity on a wide variety of nucleoside diphosphate derivatives. Of the 13 members of the family in Escherichia coli, only one, Orf180, has not been identified with a substrate, although a host of nucleoside diphosphate compounds has been tested. Several reports have noted a strong similarity in the three-dimensional structure of the unrelated enzyme, isopentenyl diphosphate isomerase (IDI) to the Nudix structure, and the report that a Nudix enzyme was involved in the synthesis of geraniol, a product of the two substrates of IDI, prompted an investigation of whether the IDI substrates, isopentenyl diphosphate (IPP), and dimethylallyl diphosphate (DAPP) could be substrates of Orf180. This article demonstrates that Orf180 does have a very low activity on IPP, DAPP, and geranyl pyrophosphate (GPP). However, several of the other Nudix enzymes with established nucleoside diphosphate substrates hydrolyze these compounds at substantial rates. In fact, some Nudix hydrolases have higher activities on IPP, DAPP, and GPP than on their signature nucleoside diphosphate derivatives.
Topics: Diphosphates; Escherichia coli; Hemiterpenes; Models, Molecular; Molecular Structure; Organophosphorus Compounds; Pyrophosphatases; Nudix Hydrolases
PubMed: 31173659
DOI: 10.1002/pro.3666 -
Brazilian Journal of Microbiology :... Sep 2021Guanosine 5'-diphosphate-3'-diphosphate (ppGpp) is a small molecule nucleotide alarmone that can accumulate under the amino acid starvation state and trigger the...
Guanosine 5'-diphosphate-3'-diphosphate (ppGpp) is a small molecule nucleotide alarmone that can accumulate under the amino acid starvation state and trigger the stringent response. This study reported the extraction of ppGpp from the Gram-positive bacteria Clavibacter michiganensis through methods using formic acid, lysozyme, or methanol. Following extraction, ppGpp was detected through ultra-high-performance liquid chromatography (UHPLC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The methanol method showed the highest extraction efficiency for ppGpp among the three methods tested. C. michiganensis cells in exponential growth phase was induced in amino acid starvation by serine hydroxamate (SHX) and used for ppGpp extraction and detection. When using the methanol extraction method, the results showed that ppGpp concentrations in SHX-treated samples were 15.645 nM, 17.656 nM, 20.372 nM, and 19.280 nM at 0 min, 15 min, 30 min and 1 h, respectively, when detected using LC-MS/MS. This is the first report on ppGpp extraction and detection in Clavibacter providing a new idea and approach for nucleotide detection and extraction in bacteria.
Topics: Amino Acids; Chromatography, Liquid; Clavibacter; Diphosphates; Guanosine Tetraphosphate; Methanol; Tandem Mass Spectrometry
PubMed: 33837930
DOI: 10.1007/s42770-021-00488-1 -
Journal of Medicinal Chemistry Jun 2023We tested a series of SQ109 analogues against and , in addition to determining their uncoupling activity. We then investigated potential protein targets, involved in...
We tested a series of SQ109 analogues against and , in addition to determining their uncoupling activity. We then investigated potential protein targets, involved in quinone and cell wall biosynthesis, using "rescue" experiments. There was little effect of menaquinone on growth inhibition by SQ109, but there were large increases in the IC of SQ109 and its analogues (up to 20×) on addition of undecaprenyl phosphate (Up), a homologue of the mycobacterial decaprenyl (C) diphosphate. Inhibition of an undecaprenyl diphosphate phosphatase, an ortholog of the mycobacterial phosphatase, correlated with cell growth inhibition, and we found that cell growth inhibition could be well predicted by using uncoupler and Up-rescue results. We also investigated whether SQ109 was metabolized inside , finding only a single metabolite, previously shown to be inactive. The results are of general interest since they help explain the mechanism of SQ109 in mycobacteria.
Topics: Humans; Antitubercular Agents; Diphosphates; Tuberculosis; Mycobacterium tuberculosis; Mycobacterium smegmatis
PubMed: 37235809
DOI: 10.1021/acs.jmedchem.3c00398 -
Cell Death & Disease Jul 2023Pathological mineralization of intervertebral disc is debilitating and painful and linked to disc degeneration in a subset of human patients. An adenosine triphosphate...
Pathological mineralization of intervertebral disc is debilitating and painful and linked to disc degeneration in a subset of human patients. An adenosine triphosphate efflux transporter, progressive ankylosis (ANK) is a regulator of extracellular inorganic pyrophosphate levels and plays an important role in tissue mineralization. However, the function of ANK in intervertebral disc has not been fully explored. Herein we analyzed the spinal phenotype of Ank mutant mice (ank/ank) with attenuated ANK function. Micro-computed tomography and histological analysis showed that loss of ANK function results in the aberrant annulus fibrosus mineralization and peripheral disc fusions with cranial to caudal progression in the spine. Vertebrae in ank mice exhibit elevated cortical bone mass and increased tissue non-specific alkaline phosphatase-positive endplate chondrocytes with decreased subchondral endplate porosity. The acellular dystrophic mineral inclusions in the annulus fibrosus were localized adjacent to apoptotic cells and cells that acquired osteoblast-like phenotype. Fourier transform infrared spectral imaging showed that the apatite mineral in the outer annulus fibrosus had similar chemical composition to that of vertebral bone. Transcriptomic analysis of annulus fibrosus and nucleus pulposus tissues showed changes in several biological themes with a prominent dysregulation of BMAL1/CLOCK circadian regulation. The present study provides new insights into the role of ANK in the disc tissue compartments and highlights the importance of local inorganic pyrophosphate metabolism in inhibiting the mineralization of this important connective tissue.
Topics: Animals; Humans; Mice; Calcinosis; Diphosphates; Intervertebral Disc; Intervertebral Disc Degeneration; Loss of Function Mutation; Phenotype; X-Ray Microtomography
PubMed: 37468461
DOI: 10.1038/s41419-023-05893-y -
Inorganic Chemistry Dec 2022The knowledge of accurate geometrical parameters from X-ray diffraction studies in the solid state of metal nucleotide is very important for understanding the...
The knowledge of accurate geometrical parameters from X-ray diffraction studies in the solid state of metal nucleotide is very important for understanding the relationship between structures and properties, including biochemical processes and even enzyme-metal-substrate interactions. The research is also very necessary to precisely and controllably design the functional materials. Here, seven types of coordination polymers of inosine 5'-diphosphate nucleotide (IDP) with transition metals, {[Zn(HIDP)(azpy)(HO)]·4HO} (), {[Cd(IDP)(bpda)]·[Cd(HO)]·11HO} (), {[Cd(IDP)(4,4'-bipy)(HO)]·6HO} (), {[Cd(IDP)(bpe)(HO)]·(Hbpe)·26HO} (), {[Cu(IDP)(azpy)(HO)]·5HO} (), {[Cu(IDP)(bpe)(HO)]·9HO} (), and {[Co(HIDP)(azpy)(HO)]·7HO} () [4,4'-bipy = 4,4'-bipyridine, azpy = 4,4'-azopyridine, bpe = 1,2-bis(4-pyridyl)ethene, and bpda = 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene], were designed, synthesized, and firmly characterized using single-crystal X-ray diffraction. The coordination patterns of the diphosphate group of IDP in these complexes were studied by crystallographic analysis, namely, open, close, and open-close hybrid types. We have investigated the diverse coordination patterns of the diphosphate group and its spatial relationship relative to the pentose ring on the basis of two conformational parameters, the pseudorotation phase angle and the degree of puckering. Crystallographic studies clearly reveal the correlation between the backbone torsion angle (ω' and φ) of the sugar-diphosphate and the conformational preference of the pentose ring, i.e., the signs of the backbone torsion angles ω' and φ are both plus (+) or minus (-), the conformation of the pentose ring is envelope form (E), while when one of the two signs is plus (+) and the other is minus (-), the pentose ring is in the twist form (T). This is the first time elucidation of the coordination pattern of diphosphate relative to the conformation of the pentose ring in nucleotide metal complexes, which are different from the other inorganic or organic diphosphate compounds. The chirality of these coordination polymers was examined by combining solid-state circular dichroism spectroscopy measurements with the explanation of their crystal structures. The results presented in this paper are very important for understanding their nucleotide coordination chemistry, their supramolecular chemistry, and even their biochemistry.
Topics: Diphosphates; Coordination Complexes; Inosine Diphosphate; Cadmium; Nucleotides; Polymers
PubMed: 36413753
DOI: 10.1021/acs.inorgchem.2c03285 -
Hemodialysis International.... Jun 2017Treatment of anemia remains an integral component in the care of patients with end stage kidney disease receiving dialysis. Currently, both erythropoiesis stimulating... (Review)
Review
Treatment of anemia remains an integral component in the care of patients with end stage kidney disease receiving dialysis. Currently, both erythropoiesis stimulating agents and iron replacement agents remain important anemia management strategies for patients undergoing hemodialysis (HD). Ferric pyrophosphate citrate (FPC) was approved by the U.S. Food and Drug Administration in January 2015 as an iron replacement product in adult patients receiving long-term maintenance HD. FPC is administered to patients on HD through the dialysate. Multicenter randomized, placebo-controlled phase three clinical studies (CRUISE 1 and 2) have found dialysate FPC to maintain hemoglobin level and iron balance in patients receiving chronic HD. Adverse events were similar in both the dialysate FPC-treated and placebo groups. Another study showed a significant reduction in the prescribed erythropoietin-stimulating agents dose at the end of treatment in the dialysate FPC-treated group compared with placebo. These studies have shown that dialysate FPC is efficacious and well tolerated. In this article, we review clinical studies evaluating the efficacy and safety of FPC and also propose a protocol for iron replacement in HD units where dialysate FPC is to be used.
Topics: Anemia; Clinical Trials as Topic; Diphosphates; Hematinics; Humans; Iron; Kidney Failure, Chronic; Renal Dialysis
PubMed: 28371161
DOI: 10.1111/hdi.12554 -
Biochemistry. Biokhimiia Mar 2020Neurodegenerative diseases are accompanied by changes in the activity of thiamine mono- and diphosphate phosphatases, but molecular identification of these mammalian...
Neurodegenerative diseases are accompanied by changes in the activity of thiamine mono- and diphosphate phosphatases, but molecular identification of these mammalian enzymes is incomplete. In this work, the protein fraction of bovine brain synaptosomes displaying phosphatase activity toward thiamine derivatives was subjected to affinity chromatography on thiamine-Sepharose. Protein fractions eluted with thiamine (pH 7.4 or 5.6), NaCl, and urea were assayed for the phosphatase activity against thiamine monophosphate (ThMP), thiamine diphosphate (ThDP), and structurally similar purine nucleotides. Proteins in each fraction were identified by mass spectrometry using the SwissProt database for all organisms because of insufficient annotation of the bovine genome. Peptides of two annotated bacterial phosphatases, alkaline phosphatase L from the DING protein family and exopolyphosphatase, were identified in the acidic thiamine eluate. The abundance of peptides of alkaline phosphatase L and exopolyphosphatase in the eluted fractions correlated with ThMPase and ThDPase activities, respectively. The elution profiles of the ThMPase and ThDPase activities differed from the elution profiles of nucleotide phosphatases, thus indicating the specificity of these enzymes toward thiamine derivatives. The search for mammalian DING phosphatases in the eluates from thiamine-Sepharose revealed X-DING-CD4, mostly eluted by the acidic thiamine solution (pH 5.6). The identified exopolyphosphatase demonstrated structural similarity with apyrases possessing the ThDPase activity. The obtained results demonstrate that mammalian DING proteins and apyrases exhibit ThMPase and ThDPase activity, respectively.
Topics: Animals; Brain; Catalytic Domain; Cattle; Chromatography, Affinity; Diphosphates; Genome; Humans; Hydrogen-Ion Concentration; Phosphoric Monoester Hydrolases; Substrate Specificity; Synaptosomes; Thiamine; Thiamine Monophosphate; Thiamine Pyrophosphate; Urea
PubMed: 32564742
DOI: 10.1134/S000629792003013X -
Journal of the American Chemical Society Feb 2024Complex bacterial glycoconjugates drive interactions between pathogens, symbionts, and their human hosts. Glycoconjugate biosynthesis is initiated at the membrane...
Complex bacterial glycoconjugates drive interactions between pathogens, symbionts, and their human hosts. Glycoconjugate biosynthesis is initiated at the membrane interface by phosphoglycosyl transferases (PGTs), which catalyze the transfer of a phosphosugar from a soluble uridine diphosphosugar (UDP-sugar) substrate to a membrane-bound polyprenol-phosphate (Pren-P). The two distinct superfamilies of PGT enzymes (polytopic and monotopic) show striking differences in their structure and mechanism. We designed and synthesized a series of uridine bisphosphonates (UBPs), wherein the diphosphate of the UDP and UDP-sugar is replaced by a substituted methylene bisphosphonate (CXY-BPs; X/Y = F/F, Cl/Cl, ()-H/F, ()-H/F, H/H, CH/CH). UBPs and UBPs incorporating an -acetylglucosamine (GlcNAc) substituent at the β-phosphonate were evaluated as inhibitors of a polytopic PGT (WecA from ) and a monotopic PGT (PglC from ). Although CHF-BP most closely mimics diphosphate with respect to its acid/base properties, the less basic CF-BP conjugate more strongly inhibited PglC, whereas the more basic CH-BP analogue was the strongest inhibitor of WecA. These surprising differences indicate different modes of ligand binding for the different PGT superfamilies, implicating a modified P-O interaction with the structural Mg. For the monoPGT enzyme, the two diastereomeric CHF-BP conjugates, which feature a chiral center at the P-CHF-P carbon, also exhibited strikingly different binding affinities and the inclusion of GlcNAc with the native α-anomer configuration significantly improved binding affinity. UBP-sugars are thus revealed as informative new mechanistic probes of PGTs that may aid development of novel antibiotic agents for the exclusively prokaryotic monoPGT superfamily.
Topics: Humans; Transferases; Uridine; Diphosphates; Glycoconjugates; Diphosphonates; Sugars; Uridine Diphosphate
PubMed: 38271668
DOI: 10.1021/jacs.3c11402 -
Drug Development Research Feb 2022The pyrophosphate mimicking groups offer rational modification of the pyrophosphate-bearing natural substrates of the overexpressed enzymes that cause the onset of... (Review)
Review
The pyrophosphate mimicking groups offer rational modification of the pyrophosphate-bearing natural substrates of the overexpressed enzymes that cause the onset of disease progression. Mainly, the modified substrate interacts differently with the enzyme active site eventually causing its deactivation, or provides the therapeutically active products at the completion of the catalytic cycle that contribute toward the inhibition of the target enzyme. Many of the pyrophosphate mimic-containing molecules serve as competitive or allosteric inhibitors of the target enzyme to achieve the desirable properties for the mitigation of the target enzyme's pathophysiology. This review presents an epigrammatic overview of the pyrophosphate mimics in medicinal chemistry.
Topics: Catalytic Domain; Chemistry, Pharmaceutical; Diphosphates
PubMed: 34506652
DOI: 10.1002/ddr.21877