Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Trisilver(I) citrate.

ABSTRACT: Trisilver(I) citrate, 3Ag(+)·C(6)H(5)O(7) (3-), was obtained by evaporation of a saturated aqueous solution of the raw material that had been obtained from sodium dihydrogen citrate and silver nitrate. It features one formula unit in the asymmetric unit. There is an intra-molecular O-H?O hydrogen bond between the OH group and one of the terminal carboxyl-ate groups. Different citrate groups are linked via the three Ag(+) ions, yielding a three-dimensional network with rather irregular [AgO(4)] polyhedra.

SUBMITTER: Fischer A

PROVIDER: S-EPMC3051445 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Trisilver(I) citrate.

Fischer Andreas A

Acta crystallographica. Section E, Structure reports online 20110122 Pt 2

Trisilver(I) citrate, 3Ag(+)·C(6)H(5)O(7) (3-), was obtained by evaporation of a saturated aqueous solution of the raw material that had been obtained from sodium dihydrogen citrate and silver nitrate. It features one formula unit in the asymmetric unit. There is an intra-molecular O-H⋯O hydrogen bond between the OH group and one of the terminal carboxyl-ate groups. Different citrate groups are linked via the three Ag(+) ions, yielding a three-dimensional network with rather irregular [AgO(4)] p ...[more]

PMID: 21522908

Similar Datasets

Orphenadrinium dihydrogen citrate.

Project description:In the title salt, C(18)H(24)NO(+)·C(6)H(7)O(7) (-), the dihedral angle between the benzene rings in the cation is 74.2 (5)°. In the crystal, anion-anion O-H⋯O hydrogen bonds and weak O-H⋯O inter-actions form infinite chains along [100]. Between these chains, cation-anion N-H-O hydrogen bonds are observed, forming an alternate pattern of cation and anion layers and leading to a two-dimensional network parallel to (100).

| S-EPMC3569781 | biostudies-literature

Allosteric role of the citrate synthase homology domain of ATP citrate lyase.

Project description:ATP citrate lyase (ACLY) is the predominant nucleocytosolic source of acetyl-CoA and is aberrantly regulated in many diseases making it an attractive therapeutic target. Structural studies of ACLY reveal a central homotetrameric core citrate synthase homology (CSH) module flanked by acyl-CoA synthetase homology (ASH) domains, with ATP and citrate binding the ASH domain and CoA binding the ASH-CSH interface to produce acetyl-CoA and oxaloacetate products. The specific catalytic role of the CSH module and an essential D1026A residue contained within it has been a matter of debate. Here, we report biochemical and structural analysis of an ACLY-D1026A mutant demonstrating that this mutant traps a (3S)-citryl-CoA intermediate in the ASH domain in a configuration that is incompatible with the formation of acetyl-CoA, is able to convert acetyl-CoA and OAA to (3S)-citryl-CoA in the ASH domain, and can load CoA and unload acetyl-CoA in the CSH module. Together, this data support an allosteric role for the CSH module in ACLY catalysis.

| S-EPMC10115795 | biostudies-literature

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions.

Project description:Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion. We hypothesise that depending on the experimental setup, extracellular citrate accumulation can have fundamentally different underlying transcriptomic landscapes. We show that varying the amount and type of supplement of an arginine auxotrophic A. niger strain results in transcriptional down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations when increased citrate production is triggered by iron limitation. By combining gene expression data obtained from these two very distinct experimental setups with hidden Markov models and transporter homology approaches, we were able to compile a shortlist of the most likely citrate transporter candidates. Two candidates (An17g01710 and An09g06720m.01) were heterologously expressed in the yeast Saccharomyces cerevisiae, and one of the resultant mutants showed the ability to secrete citrate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we demonstrate how a comparative transcriptomics approach complemented with further bioinformatics analyses can be used to pinpoint a fungal citrate exporter.

| S-EPMC6502548 | biostudies-literature

Sodium dipotassium citrate, NaK2C6H5O7.

Project description:The crystal structure of sodium dipotassium citrate, Na(+)·2K(+)·C6H5O7 (3-), has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The Na(+) and one of the K(+) cations are six-coordinate, with bond-valence sums of 1.13 and 0.92 valence units, respectively, while another crystallographically independent K(+) cation is seven-coordinate with a bond-valence sum of 1.20. The [KO6] and [KO7] polyhedra share edges and corners to form layers perpendicular to the b axis. The distorted [NaO6] octa-hedra share edges to form chains along the a axis. The result is a three-dimensional network. The only O-H⋯O hydrogen bond is an intra-molecular one between the hy-droxy group and a terminal carboxyl-ate group.

| S-EPMC4778822 | biostudies-literature

Citrate-stabilized gold nanorods.

Project description:Stable aqueous dispersions of citrate-stabilized gold nanorods (cit-GNRs) have been prepared in scalable fashion by surfactant exchange from cetyltrimethylammonium bromide (CTAB)-stabilized GNRs, using polystyrenesulfonate (PSS) as a detergent. The surfactant exchange process was monitored by infrared spectroscopy, surface-enhanced Raman scattering (SERS), and X-ray photoelectron spectroscopy (XPS). The latter established the quantitative displacement of CTAB (by PSS) and of PSS (by citrate). The Cit-GNRs are indefinitely stable at low ionic strength, and are conducive to further ligand exchange without loss of dispersion stability. The reliability of the surface exchange process supports the systematic analysis of ligand structure on the hydrodynamic size of GNRs, as described in a companion paper.

| S-EPMC4334258 | biostudies-literature

Trisodium citrate, Na3(C6H5O7).

Project description:The crystal structure of anhydrous tris-odium citrate, Na3(C6H5O7), has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory (DFT). There are two independent five-coordinate Na(+) and one six-coordinate Na(+) cations in the asymmetric unit. The [NaO5] and [NaO6] polyhedra share edges and corners to form a three-dimensional framework. There are channels parallel to the a and b axes in which the remainder of the citrate anions reside. The only hydrogen bonds are an intra-molecular one between the hy-droxy group and one of the terminal carboxyl-ate O atoms and an intermolecular one between a methylene group and the hydroxyl O atom.

| S-EPMC4908562 | biostudies-literature

Selective autophagic degradation of ATP citrate lyase maintains citrate homeostasis and promotes oocyte maturation

Project description:Autophagy is a cellular and energy homeostatic mechanism that contributes to maintain the number of primordial follicles, germ cell survival, and anti-ovarian aging. However, it remains unknown whether autophagy in granulosa cells affects the oocyte maturation. Here, we show a clear tendency of reduced autophagy level in human granulosa cell from women of advanced maternal age, implying a potential negative correlation between autophagy level and oocyte quality. We therefore established a co-culture system and show that either pharmacological inhibition or genetic ablation of autophagy in granulosa cells negatively affect the oocyte quality and fertilization ability. Moreover, our metabolomics analysis indicates that the adverse impact of autophagy impairment on oocyte quality is mediated by downregulated citrate levels, while exogenous supplementation of citrate can significantly restore the oocyte maturation. In molecular level, we found ATP citrate lyase (Acly), which is a crucial enzyme catalyzing the cleavage of citrate, was preferentially associated with K63-linked ubiquitin chains and recognized by the autophagy receptor protein SQSTM1/p62 for the selective autophagic degradation. In human follicles, autophagy levels in granulosa cells was downregulated with maternal aging, accompanied by decreased citrate in the follicular fluid, implying a potential correlation between citrate metabolism and oocyte quality. We also show that elevated citrate levels in porcine follicular fluid promote oocyte maturation. Collectively, our data reveal that autophagy in granulosa cells is a beneficial mechanism to maintain a certain degree of citrate by selectively targeting Acly during oocyte maturation.

2023-01-09 | GSE190697 | GEO

citrate vs nitrate Reducing cultures

Project description:The effect of nitrate reduction (anaerobic cultivation in the presence of heme, vitamin K2 and nitrate) was compared with anaerobic cultivation supplemented with citrate (Lactobacillus plantarum). The medium was chemically defined medium with mannitol as main carbon source

2010-01-01 | GSE18339 | GEO

Citrate, low pH and amino acid limitation induce citrate utilization in Lactococcus lactis biovar diacetylactis.

Project description:In Lactococcus lactis subsp. lactis biovar diacetylactis, citrate transport is facilitated by the plasmid-encoded citrate permease (CitP). In this work, we analysed regulation of citrate utilization by pH, nutrient limitation and the presence of citrate at four different levels: (i) plasmid copy number, (ii) citP transcription, (iii) citP mRNA processing and (iv) citrate utilization capacity. Citrate was supplied as cosubstrate together with lactose. The citP gene is known to be induced in cells grown at low pH. However, we demonstrated that transcription of citP was even higher in the presence of citrate (3.8-fold compared with 2.0-fold). The effect of citrate has been overlooked by other researchers because they determined the effect of citrate using M17 medium, which already contains 0.80 ± 0.07 mM citrate. The plasmid copy number increased in cells grown under amino acid limitation (1.6-fold) and/or at low pH (1.4-fold). No significant differences in citP mRNA processing were found. Citrate utilization rates increased from approximately 1 to 65 ?mol min-1 gDW-1 from lowest to highest citP expression. Acetoin formation increased during growth in an acidic environment due to induction of the acetoin pathway. Quantification of the relative contributions allowed us to construct a model for regulation of citrate utilization in L. lactis biovar diacetylactis. This knowledge will help to select conditions to improve flavour formation from citrate.

| S-EPMC5812246 | biostudies-literature

Identification of the citrate-binding site of human ATP-citrate lyase using X-ray crystallography.

Project description:ATP-citrate lyase (ACLY) catalyzes the conversion of citrate and CoA into acetyl-CoA and oxaloacetate, coupled with the hydrolysis of ATP. In humans, ACLY is the cytoplasmic enzyme linking energy metabolism from carbohydrates to the production of fatty acids. In situ proteolysis of full-length human ACLY gave crystals of a truncated form, revealing the conformations of residues 2-425, 487-750, and 767-820 of the 1101-amino acid protein. Residues 2-425 form three domains homologous to the beta-subunit of succinyl-CoA synthetase (SCS), while residues 487-820 form two domains homologous to the alpha-subunit of SCS. The crystals were grown in the presence of tartrate or the substrate, citrate, and the structure revealed the citrate-binding site. A loop formed by residues 343-348 interacts via specific hydrogen bonds with the hydroxyl and carboxyl groups on the prochiral center of citrate. Arg-379 forms a salt bridge with the pro-R carboxylate of citrate. The pro-S carboxylate is free to react, providing insight into the stereospecificity of ACLY. Because this is the first structure of any member of the acyl-CoA synthetase (NDP-forming) superfamily in complex with its organic acid substrate, locating the citrate-binding site is significant for understanding the catalytic mechanism of each member, including the prototype SCS. Comparison of the CoA-binding site of SCSs with the similar structure in ACLY showed that ACLY possesses a different CoA-binding site. Comparisons of the nucleotide-binding site of SCSs with the similar structure in ACLY indicates that this is the ATP-binding site of ACLY.

| S-EPMC2930740 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data