Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystal structure of an archaeal CorB magnesium transporter.

ABSTRACT: CNNM/CorB proteins are a broadly conserved family of integral membrane proteins with close to 90,000 protein sequences known. They are associated with Mg²⁺ transport but it is not known if they mediate transport themselves or regulate other transporters. Here, we determine the crystal structure of an archaeal CorB protein in two conformations (apo and Mg²⁺-ATP bound). The transmembrane DUF21 domain exists in an inward-facing conformation with a Mg²⁺ ion coordinated by a conserved π-helix. In the absence of Mg²⁺-ATP, the CBS-pair domain adopts an elongated dimeric configuration with previously unobserved domain-domain contacts. Hydrogen-deuterium exchange mass spectrometry, analytical ultracentrifugation, and molecular dynamics experiments support a role of the structural rearrangements in mediating Mg²⁺-ATP sensing. Lastly, we use an in vitro, liposome-based assay to demonstrate direct Mg²⁺ transport by CorB proteins. These structural and functional insights provide a framework for understanding function of CNNMs in Mg²⁺ transport and associated diseases.

SUBMITTER: Chen YS

PROVIDER: S-EPMC8242095 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus.

Project description:Ammonium transporters (Amts) are integral membrane proteins found in all kingdoms of life that fulfill an essential function in the uptake of reduced nitrogen for biosynthetic purposes. Amt-1 is one of three Amts encoded in the genome of the hyperthermophilic archaeon Archaeoglobus fulgidus. The crystal structure of Amt-1 shows a compact trimer with 11 transmembrane helices per monomer and a central channel for substrate conduction in each monomer, similar to the known crystal structure of AmtB from Escherichia coli. Xenon derivatization has been used to identify apolar regions of Amt-1, emphasizing not only the hydrophobicity of the substrate channel but also the unexpected presence of extensive internal cavities that should be detrimental for protein stability. The substrates ammonium and methylammonium have been used for cocrystallization experiments with Amt-1, but the identification of binding sites that are distinct from water positions is not unambiguous. The well ordered cytoplasmic C terminus of the protein in the Amt-1 structure has allowed for the construction of a docking model between Amt-1 and a homology model for its physiological interaction partner, the P(II) protein GlnB-1. In this model, GlnB-1 binds tightly to the cytoplasmic face of the transporter, effectively blocking conduction through the three individual substrate channels.

| S-EPMC1257715 | biostudies-literature

Crystal structure of a dimeric ?-diketiminate magnesium complex.

Project description:The solid-state structure of a dimeric ?-diketiminate magnesium(II) complex is discussed. The compound, di-?-iodido-bis-[(-{4-amino-1,5-bis-[2,6-bis-(propan-2-yl)phen-yl]pent-3-en-2-yl-idene}aza-nido-?2N,N')magnesium(II)] toluene sesquisolvate, [Mg2(C29H41N2)2I2]·1.5C7H8, crystallizes as two independent mol-ecules, each with 2/m crystallographic site symmetry, located at Wyckoff sites 2c and 2d. These have symmetry-equivalent magnesium atoms bridged by ?-iodide ligands with very similar Mg-I distances. The two Mg atoms are located slightly below (?0.5?Å) the least-squares plane defined by N-C-C-N atoms in the ligand scaffold, and are approximately tetra-hedrally coordinated. One and one-half toluene solvent mol-ecules are disordered with respect to mirror-site symmetry at Wyckoff sites 4i and 2a, respectively. In the former case, two toluene mol-ecules inter-act in an off-center parallel stacking arrangement; the shortest C to C' (?-?) distance of 3.72?(1)?Å was measured for this inter-action.

| S-EPMC5137601 | biostudies-literature

Crystal structure and characterization of magnesium carbonate chloride heptahydrate.

Project description:MgCO3·MgCl2·7H2O is the only known neutral magnesium carbonate containing chloride ions at ambient conditions. According to the literature, only small and twinned crystals of this double salt could be synthesised in a concentrated solution of MgCl2. For the crystal structure solution, single-crystal diffraction was carried out at a synchrotron radiation source. The monoclinic crystal structure (space group Cc) exhibits double chains of MgO octahedra linked by corners, connected by carbonate units and water molecules. The chloride ions are positioned between these double chains parallel to the (100) plane. Dry MgCO3·MgCl2·7H2O decomposes in the air to chlorartinite, Mg2(OH)Cl(CO3)·nH2O (n = 2 or 3). This work includes an extensive characterization of the title compound by powder X-ray diffraction, thermal analysis, SEM and vibrational spectroscopy.

| S-EPMC7404730 | biostudies-literature

The first crystal structure of an archaeal helical repeat protein.

Project description:The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 A resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten alpha-helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein.

| S-EPMC1952456 | biostudies-literature

Crystal structure of the CorA Mg2+ transporter.

Project description:The magnesium ion, Mg2+, is essential for myriad biochemical processes and remains the only major biological ion whose transport mechanisms remain unknown. The CorA family of magnesium transporters is the primary Mg2+ uptake system of most prokaryotes and a functional homologue of the eukaryotic mitochondrial magnesium transporter. Here we determine crystal structures of the full-length Thermotoga maritima CorA in an apparent closed state and its isolated cytoplasmic domain at 3.9 A and 1.85 A resolution, respectively. The transporter is a funnel-shaped homopentamer with two transmembrane helices per monomer. The channel is formed by an inner group of five helices and putatively gated by bulky hydrophobic residues. The large cytoplasmic domain forms a funnel whose wide mouth points into the cell and whose walls are formed by five long helices that are extensions of the transmembrane helices. The cytoplasmic neck of the pore is surrounded, on the outside of the funnel, by a ring of highly conserved positively charged residues. Two negatively charged helices in the cytoplasmic domain extend back towards the membrane on the outside of the funnel and abut the ring of positive charge. An apparent Mg2+ ion was bound between monomers at a conserved site in the cytoplasmic domain, suggesting a mechanism to link gating of the pore to the intracellular concentration of Mg2+.

| S-EPMC3836678 | biostudies-literature

Crystal structure of a eukaryotic phosphate transporter.

Project description:Phosphate is crucial for structural and metabolic needs, including nucleotide and lipid synthesis, signalling and chemical energy storage. Proton-coupled transporters of the major facilitator superfamily (MFS) are essential for phosphate uptake in plants and fungi, and also have a function in sensing external phosphate levels as transceptors. Here we report the 2.9?Å structure of a fungal (Piriformospora indica) high-affinity phosphate transporter, PiPT, in an inward-facing occluded state, with bound phosphate visible in the membrane-buried binding site. The structure indicates both proton and phosphate exit pathways and suggests a modified asymmetrical 'rocker-switch' mechanism of phosphate transport. PiPT is related to several human transporter families, most notably the organic cation and anion transporters of the solute carrier family (SLC22), which are implicated in cancer-drug resistance. We modelled representative cation and anion SLC22 transporters based on the PiPT structure to surmise the structural basis for substrate binding and charge selectivity in this important family. The PiPT structure demonstrates and expands on principles of substrate transport by the MFS transporters and illuminates principles of phosphate uptake in particular.

| S-EPMC3678552 | biostudies-literature

Crystal structure of magnesium copper(II) bis-[orthophosphate(V)] monohydrate.

Project description:Single crystals of magnesium copper(II) bis-[orthophosphate(V)] monohydrate, Mg1.65Cu1.35(PO4)2·H2O, were grown under hydro-thermal conditions. The crystal structure is formed by three types of cationic sites and by two unique (PO4)(3-) anions. One site is occupied by Cu(2+), the second site by Mg(2+)and the third site by a mixture of the two cations with an Mg(2+):Cu(2+) occupancy ratio of 0.657 (3):0.343 (3). The structure is built up from more or less distorted [MgO6] and [(Mg/Cu)O5(H2O)] octa-hedra, [CuO5] square-pyramids and regular PO4 tetra-hedra, leading to a framework structure. Within this framework, two types of layers parallel to (-101) can be distinguished. The first layer is formed by [Cu2O8] dimers linked to PO4 tetra-hedra via common edges. The second, more corrugated layer results from the linkage between [(Cu/Mg)2O8(H2O)2] dimers and [MgO6] octa-hedra by common edges. The PO4 units link the two types of layers, leaving space for channels parallel [101], into which the H atoms of the water mol-ecules protrude. The latter are involved in O-H⋯O hydrogen-bonding inter-actions (one bifurcated) with framework O atoms across the channels.

| S-EPMC4331867 | biostudies-literature

Crystal structure of a phosphorylation-coupled saccharide transporter.

Project description:Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

| S-EPMC3201810 | biostudies-literature

Crystal structure of a potassium ion transporter, TrkH.

Project description:The TrkH/TrkG/KtrB proteins mediate K(+) uptake in bacteria and probably evolved from simple K(+) channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K(+) channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K(+) and Rb(+) over smaller ions such as Na(+) or Li(+). Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K(+) flux. These results reveal the molecular basis of K(+) selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.

| S-EPMC3077569 | biostudies-literature

Crystal structure of the bacterial nucleoside transporter Tsx.

Project description:Tsx is a nucleoside-specific outer membrane (OM) transporter of Gram-negative bacteria. We present crystal structures of Escherichia coli Tsx in the absence and presence of nucleosides. These structures provide a mechanism for nucleoside transport across the bacterial OM. Tsx forms a monomeric, 12-stranded beta-barrel with a long and narrow channel spanning the outer membrane. The channel, which is shaped like a keyhole, contains several distinct nucleoside-binding sites, two of which are well defined. The base moiety of the nucleoside is located in the narrow part of the keyhole, while the sugar occupies the wider opening. Pairs of aromatic residues and flanking ionizable residues are involved in nucleoside binding. Nucleoside transport presumably occurs by diffusion from one binding site to the next.

| S-EPMC514505 | 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