scholarly journals The π-helix formation between Asp369 and Thr375 as a key factor in E1-E2 conformational change of Na+/K+-ATPase

2009 ◽  
pp. 583-589
Author(s):  
G Tejral ◽  
L Koláčná ◽  
W Schoner ◽  
E Amler
Keyword(s):  
Molecular Modeling ◽  
Atpase Activity ◽  
Binding Site ◽  
Conformational Change ◽  
Phosphorylation Site ◽  
Hinge Region ◽  
Atp Binding Site ◽  
Helix Formation ◽  
Key Factor ◽  
P Domain

Molecular modeling of the H4-H5-loop of the α2 isoform of Na+/K+- ATPase in the E1 and E2 conformations revealed that twisting of the nucleotide (N) domain toward the phosphorylation (P) domain is connected with the formation of a short π-helix between Asp369 and Thr375. This conformational change close to the hinge region between the N-domain and the P-domain could be an important event leading to a bending of the N-domain by 64.7° and to a shortening of the distance between the ATP binding site and the phosphorylation site (Asp369) by 1.22 nm from 3.22 nm to 2.00 nm. It is hypothesized that this shortening mechanism is involved in the Na+-dependent formation of the Asp369 phospho-intermediate as part of the overall Na+/K+- ATPase activity.

scholarly journals Comparative modeling of the H4-H5 loop of the α2-isoform of Na+/K+-ATPase α-subunit in the E1 conformation

2007 ◽  
pp. S143-S151
Author(s):  
G Tejral ◽  
L Koláčná ◽  
A Kotyk ◽  
E Amler
Keyword(s):  
Binding Site ◽  
Phosphorylation Site ◽  
Comparative Modeling ◽  
Atp Binding ◽  
Beta Sheet ◽  
Alpha Helices ◽  
Α Subunit ◽  
Atp Binding Site ◽  
P Domain ◽  
Alpha Carbon

Restraint-based comparative modeling was used for calculation and visualization of the H4-H5-loop of Na+/K+-ATPase from mouse brain (Mus musculus, adult male brain, alpha2-isoform) between the amino acid residues Cys 336 and Arg 758 in the E1 conformation The structure consists of two well separated parts. The N-domain is formed by a seven-stranded antiparallel beta-sheet with two additional beta-strands and five alpha-helices sandwiching it, the P-domain is composed of a typical Rossman fold. The ATP-binding site was found on the N-domain to be identical in both alpha2- and alpha1-isoforms. The phosphorylation Asp 369 residue was found in the central part of the P-domain, located at the C-terminal end of the central beta-sheet. The distance between the alpha-carbon of Phe 475 at the ATP-binding site and the alpha-carbon of Asp 369 at the phosphorylation site is 3.22 nm. A hydrogen bond between the oxygen atom of Asp 369 and the nitrogen atom of Lys 690 was clearly detected and assumed to play a key role in maintaining the proper structure of the phosphorylaton site in E1 conformation.

scholarly journals Effect of Heldanamycin Binding on the Thr90 Phosphorylation Site of Hsp90

2021 ◽  
Vol 4 (3) ◽  
pp. e00145
Author(s):  
K.A. Shcherbakov ◽  
D.S. Shcherbinin ◽  
A.V. Veselovsky
Keyword(s):  
Prostate Cancer ◽  
Transcription Factor ◽  
Androgen Receptor ◽  
Molecular Modeling ◽  
Phosphorylation Site ◽  
Heat Shock Protein 90 ◽  
Hsp90 Inhibitor ◽  
Inhibitor Binding ◽  
Atp Binding Site ◽  
Modeling Methods

Prostate cancer is hormone-dependent and the androgen receptor (AR) is involved in its development. AR is a transcription factor that is activated by ligand binding, result in its translocation into the nucleus, where it initiates gene transcription. In an inactive state in cytoplasm AR exists as a complex with heat shock protein 90 (HSP90) and some other proteins. When the agonist binds, a conformational change in AR occurs, resulting in HSP90 and other chaperones dissociating. Recently it has been shown that for the dissociation of the HSP90-AR complex and the translocation of the latter into the nucleus, phosphorylation of the Thr-90 residue of the N-terminal domain of HSP90 is necessary. In this work, the effect of the HSP90 inhibitor, heldanamycin, interacting with the ATP-binding site, on the Thr90 phosphorylation site was investigated by molecular modeling methods. It has been shown that inhibitor binding slightly affects the size and mobility of cavity around Thr90. It is suggested that inhibitor binding to HSP90 does not result in changing the protein structure and does not influence on protein phosphorylation, and partially explains low effectiveness of such type of drugs in the therapy of prostate cancer.

Competitive Inhibition of Quercetin and Apigenin at the ATP Binding site of D-Alanine-D-Alanine Ligase of Helicobacter pylori – A Molecular Modeling Approach

2019 ◽  
Vol 7 (5) ◽  
pp. 340-348 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Chandrabose Selvaraj ◽  
Bolin Kumar Knowar ◽  
Sanjeev Kumar Singh ◽  
Chingakham Brajakishor Singh ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Molecular Modeling ◽  
Binding Site ◽  
Competitive Inhibition ◽  
Atp Binding ◽  
Atp Binding Site ◽  
Modeling Approach

scholarly journals Effect of salinity on modulation by ATP, protein kinases and FXYD2 peptide of gill (Na+, K+)-ATPase activity in the swamp ghost crab Ucides cordatus (Brachyura, Ocypodidae)

2020 ◽  
Author(s):  
Francisco A. Leone ◽  
Malson N. Lucena ◽  
Leonardo M. Fabri ◽  
Daniela P. Garçon ◽  
Carlos F.L. Fontes ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Binding Site ◽  
Protein Kinases ◽  
Atp Binding ◽  
List Type ◽  
Inhibit Activity ◽  
Ucides Cordatus ◽  
Atp Binding Site ◽  
High Affinity ◽  
Endogenous Protein

ABSTRACTThe gill (Na+, K+)-ATPase is the main enzyme that underpins osmoregulatory ability in crustaceans that occupy biotopes like mangroves, characterized by salinity variation. We evaluated osmotic and ionic regulatory ability in the semi-terrestrial mangrove crab Ucides cordatus after 10-days acclimation to different salinities. We also analyzed modulation by exogenous FXYD2 peptide and by endogenous protein kinases A and C, and Ca2+- calmodulin-dependent kinase of (Na+, K+)-ATPase activity. Hemolymph osmolality was strongly hyper-/hypo-regulated in crabs acclimated at 2 to 35 ‰S. Cl- was well hyper-/hypo- regulated although Na+ much less so, becoming iso-natremic at high salinity. (Na+, K+)- ATPase activity was greatest in isosmotic crabs (26 ‰S), diminishing progressively from 18 and 8 ‰S (≈0.5 fold) to 2 ‰S (0.04-fold), and decreasing notably at 35 ‰S (0.07-fold). At low salinity, the (Na+, K+)-ATPase exhibited a low affinity ATP-binding site that showed Michaelis-Menten behavior. Above 18 ‰S, an additional, high affinity ATP-binding site, corresponding to 10-20% of total (Na+, K+)-ATPase activity appeared. Activity is stimulated by exogenous pig kidney FXYD2 peptide, while endogenous protein kinases A and C and Ca2+/calmodulin-dependent kinase all inhibit activity. This is the first demonstration of inhibitory phosphorylation of a crustacean (Na+, K+)-ATPase by Ca2+/calmodulin-dependent kinase. Curiously, hyper-osmoregulation in U. cordatus shows little dependence on gill (Na+, K+)-ATPase activity, suggesting a role for other ion transporters. These findings reveal that the salinity acclimation response in U. cordatus consists of a suite of osmoregulatory and enzymatic adjustments that maintain its osmotic homeostasis in a challenging, mangrove forest environment.Graphical abstractHighlightsGill (Na+, K+)-ATPase activity is greatest in isosmotic crabs, diminishing in lower and higher salinities.A high affinity ATP-binding site (10-20% of total activity) is exposed above 18 ‰S.Exogenous FXYD2 peptide stimulates activity; endogenous PKA, PKC and CaMK inhibit activity.First demonstration of inhibitory phosphorylation of crustacean (Na+, K+)-ATPase by CaMK.Hyper-osmoregulation shows little dependence on (Na+, K+)-ATPase activity.

scholarly journals Computer modelling reveals new conformers of the ATP binding loop of Na+/K+-ATPase involved in the transphosphorylation process of the sodium pump

2017 ◽  
Author(s):  
Gracian Tejral ◽  
Bruno Sopko ◽  
Alois Necas ◽  
Wilhelm Schoner ◽  
Evzen Amler
Keyword(s):  
Molecular Modeling ◽  
Computer Modelling ◽  
Phosphorylation Site ◽  
Atp Binding ◽  
Cytoplasmic Loop ◽  
Α Subunit ◽  
Closed Conformation ◽  
Open Conformation ◽  
P Domain ◽  
P Type

Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, 3-dimensional molecular structure analysis of P-type ATPases reveals that binding of ATP to the N-domain connected by a hinge to the P-domain is much too far away from the Asp369 to allow the transfer of ATP’s terminal phosphate to its aspartyl-phosphorylation site. In order to get information how the transfer of the γ‑phosphate group of ATP to the Asp369 is achieved, analogous molecular modeling of the M4-M5 loop of ATPase was performed using the crystal data of Na+/K+-ATPase of different species. Analogous molecular modeling of the cytoplasmic loop between Thr338 and Ile760 of the α2-subunit of Na+/K+-ATPase and the analysis of distances between the ATP binding site and phosphorylation site revealed the existence of 2 ATP binding sites in the open conformation, the first one close to Phe475 in the N-domain, the other one close to Asp369 in the P-domain. However, binding of Mg2+•ATP to any of these sites in the “open conformation” may not lead to phosphorylation of Asp369. Additional conformations of the cytoplasmic loop were found wobbling between “open conformation” <==> “semi-open conformation <==> “closed conformation” in the absence of 2Mg2+•ATP. The cytoplasmic loop’s conformational change to the “semi-open conformation” -- characterized by a hydrogen bond between Arg543 and Asp611 -- triggers by binding of 2Mg2+•ATP to a single ATP site and conversion to the “closed conformation” the phosphorylation of Asp369 in the P-domain, and hence the start of Na+/K+-activated ATP hydrolysis.

ATP-Binding Site of Human Brain Hexokinase As Studied by Molecular Modeling and Site-Directed Mutagenesis†

Biochemistry ◽  
1996 ◽  
Vol 35 (40) ◽  
pp. 13157-13164 ◽  
Author(s):  
Chenbo Zeng ◽  
Alexander E. Aleshin ◽  
Jason B. Hardie ◽  
Robert W. Harrison ◽  
Herbert J. Fromm
Keyword(s):  
Molecular Modeling ◽  
Human Brain ◽  
Binding Site ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Atp Binding ◽  
Atp Binding Site

scholarly journals Molecular characterization of a sarco(endo)plasmic reticulum Ca2+-ATPase gene from Paramecium tetraurelia and localization of its gene product to sub-plasmalemmal calcium stores

1998 ◽  
Vol 334 (1) ◽  
pp. 31-38 ◽  
Author(s):  
Karin HAUSER ◽  
Nada PAVLOVIC ◽  
Roland KISSMEHL ◽  
Helmut PLATTNER
Keyword(s):  
Nucleotide Sequence ◽  
Molecular Mass ◽  
Binding Site ◽  
Phosphorylation Site ◽  
Atp Binding ◽  
Calcium Stores ◽  
Paramecium Tetraurelia ◽  
Conserved Domains ◽  
Atp Binding Site ◽  
Plasmic Reticulum

A cDNA encoding the gene for a sarco(endo)plasmic reticulum-type Ca2+-ATPase (SERCA) was isolated from a cDNA library of Paramecium tetraurelia by using degenerated primers according to conserved domains of SERCA-type ATPases. The identified nucleotide sequence (PtSERCA) is 3114 nucleotides in length with an open reading frame of 1037 amino acids. An intron of only 22 nucleotides occurs. Homology searches for the deduced amino acid sequence revealed 38–49% similarity to SERCA-type ATPases from organisms ranging from protozoans to mammals, with no more similarity to some parasitic protozoa of the same phylum. The calculated molecular mass of the encoded protein is 114.7 kDa. It contains the typical 10 transmembrane domains of SERCA-type ATPases and other conserved domains, such as the phosphorylation site and the ATP binding site. However, there are no binding sites for phospholamban and thapsigargin present in the PtSERCA. Antibodies raised against a cytoplasmic loop peptide between the phosphorylation site and the ATP binding site recognize on Western blots a protein of 106 kDa, exclusively in the fraction of sub-plasmalemmal calcium stores (‘alveolar sacs’). In immunofluorescence studies the antibodies show labelling exclusively in the cell cortex of permeabilized cells in a pattern characteristic of the arrangement of alveolar sacs. When alveolar sacs where tested for phosphoenzyme-intermediate formation a phosphoprotein of the same molecular mass (106 kDa) could be identified. The nucleotide sequence data reported will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession number Y17496.

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