scholarly journals Introduction of a Carboxyl Group in the First Transmembrane Helix of Escherichia coliF1Fo ATPase Subunit c and Cytoplasmic pH Regulation

2001 ◽  
Vol 183 (5) ◽  
pp. 1524-1530 ◽  
Author(s):  
Phil C. Jones
Keyword(s):  
Ph Regulation ◽  
Transmembrane Helix ◽  
Binding Pocket ◽  
Side Chain ◽  
Ion Binding ◽  
Cytoplasmic Ph ◽  
Wild Type ◽  
Atpase Subunit ◽  
Subunit C ◽  
E Coli

ABSTRACT The multicopy subunit c of the H+-transporting F1Fo ATP synthase of Escherichia coli folds across the membrane as a hairpin of two hydrophobic α helices. The subunits interact in a front-to-back fashion, forming an oligomeric ring with helix 1 packing in the interior and helix 2 at the periphery. A conserved carboxyl, Asp61 in E. coli, centered in the second transmembrane helix is essential for H+ transport. A second carboxylic acid in the first transmembrane helix is found at a position equivalent to Ile28 in several bacteria, some the cause of serious infectious disease. This side chain has been predicted to pack proximal to the essential carboxyl in helix 2. It appears that in some of these bacteria the primary function of the enzyme is H+pumping for cytoplasmic pH regulation. In this study, Ile28was changed to Asp and Glu. Both mutants were functional. However, unlike the wild type, the mutants showed pH-dependent ATPase-coupled H+ pumping and passive H+ transport through Fo. The results indicate that the presence of a second carboxylate enables regulation of enzyme function in response to cytoplasmic pH and that the ion binding pocket is aqueous accessible. The presence of a single carboxyl at position 28, in mutants I28D/D61G and I28E/D61G, did not support growth on a succinate carbon source. However, I28E/D61G was functional in ATPase-coupled H+transport. This result indicates that the side chain at position 28 is part of the ion binding pocket.

Mutational analysis of the glucagon receptor: similarities with the vasoactive intestinal peptide (VIP)/pituitary adenylate cyclase-activating peptide (PACAP)/secretin receptors for recognition of the ligand's third residue

2002 ◽  
Vol 362 (2) ◽  
pp. 389-394 ◽  
Author(s):  
Jason PERRET ◽  
Mélanie VAN CRAENENBROECK ◽  
Ingrid LANGER ◽  
Pascale VERTONGEN ◽  
Françoise GREGOIRE ◽  
...  
Keyword(s):  
Vasoactive Intestinal Peptide ◽  
Functional Properties ◽  
Mutational Analysis ◽  
Transmembrane Helix ◽  
Binding Pocket ◽  
Side Chain ◽  
Wild Type ◽  
Glucagon Receptor ◽  
Pituitary Adenylate Cyclase ◽  
In The Wild

Receptor recognition by the Asp3 residues of vasoactive intestinal peptide and secretin requires the presence of a lysine residue close to the second transmembrane helix (TM2)/first extracellular loop junction and an ionic bond with an arginine residue in TM2. We tested whether the glucagon Gln3 residue recognizes the equivalent positions in its receptor. Our data revealed that the binding and functional properties of the wild-type glucagon receptor and the K188R mutant were not significantly different, whereas all agonists had markedly lower potencies and affinities at the I195K mutated receptor. In contrast, glucagon was less potent and the Asp3-, Asn3- and Glu3-glucagon mutants were more potent and efficient at the double-mutated K188R/I195K receptor. Furthermore, these alterations were selective for position 3 of glucagon, as shown by the functional properties of the mutant Glu9- and Lys15-glucagon. Our results suggest that although the Gln3 residue of glucagon did not interact with the equivalent binding pocket as the Asp3 residue of vasoactive intestinal peptide or secretin, the Asp3-glucagon analogue was able to interact with position 188 of the K188R/I195K glucagon receptor. Nevertheless, the Gln3 side chain of glucagon probably binds very close to this region in the wild-type receptor.

scholarly journals Mutant tryptophan aporepressors with altered specificities of corepressor recognition.

Genetics ◽  
1991 ◽  
Vol 128 (1) ◽  
pp. 29-35
Author(s):  
D N Arvidson ◽  
M Shapiro ◽  
P Youderian
Keyword(s):  
Dna Binding ◽  
Binding Pocket ◽  
Side Chain ◽  
Wild Type ◽  
Mutant Proteins ◽  
Naturally Occurring ◽  
Repressor Complex ◽  
Genes Encoding ◽  
Active Repressor

Abstract The Escherichia coli trpR gene encodes tryptophan aporepressor, which binds the corepressor ligand, L-tryptophan, to form an active repressor complex. The side chain of residue valine 58 of Trp aporepressor sits at the bottom of the corepressor (L-tryptophan) binding pocket. Mutant trpR genes encoding changes of Val58 to the other 19 naturally occurring amino acids were made. Each of the mutant proteins requires a higher intracellular concentration of tryptophan for activation of DNA binding than wild-type aporepressor. Whereas wild-type aporepressor is activated better by 5-methyltryptophan (5-MT) than by tryptophan, Ile58 and other mutant aporepressors prefer tryptophan to 5-MT as corepressor, and Ala58 and Gly58 prefer 5-MT much more strongly than wild-type aporepressor in vivo. These mutant aporepressors are the first examples of DNA-binding proteins with altered specificities of cofactor recognition.

A study of the relationships of interactions between Asp-201, Na+ or K+, and galactosyl C6 hydroxyl and their effects on binding and reactivity of β-galactosidase

2004 ◽  
Vol 82 (2) ◽  
pp. 275-284 ◽  
Author(s):  
Julia Xu ◽  
Mary A.A McRae ◽  
Scott Harron ◽  
Beatrice Rob ◽  
Reuben E Huber
Keyword(s):  
Physical Properties ◽  
Negative Charge ◽  
Binding Pocket ◽  
Side Chain ◽  
Wild Type ◽  
Sodium Potassium ◽  
The Difference ◽  
Potassium Binding ◽  
Covalent Intermediate ◽  
Catalytic Effects

The interactions between Na+ (and K+) and Asp-201 of β-galactosidase were studied. Analysis of the changes in Km and Vmax showed that the Kd for Na+ of wild type β-galactosidase (0.36 ± 0.09 mM) was about 10× lower than for K+ (3.9 ± 0.6 mM). The difference is probably because of the size and other physical properties of the ions and the binding pocket. Decreases of Km as functions of Na+ and K+ for oNPG and pNPG and decreases of the Ki of both shallow and deep mode inhibitors were similar, whereas the Km and Ki of substrates and inhibitors without C6 hydroxyls remained constant. Thus, Na+ and K+ are important for binding galactosyl moieties via the C6 hydroxyl throughout catalysis. Na+ and K+ had lesser effects on the Vmax. The Vmax of pNPF and pNPA (substrates that lack a C6 hydroxyl) did not change upon addition of Na+ or K+, showing that the catalytic effects are also mediated via the C6 hydroxyl. Arrhenius plots indicated that Na+, but not K+, caused k3 (degalactosylation) to increase. Na+ also caused the k2 (galactosylation) with oNPG, but not with pNPG, to increase. In contrast, K+ caused the k2 values with both oNPG and pNPG to increase. Na+ and K+ mainly altered the entropies of activation of k2 and k3 with only small effects on the enthalpies of activation. This strongly suggests that only the positioning of the substrate, transition states, and covalent intermediate are altered by Na+ and K+. Further evidence that positioning is important was that substitution of Asp-201 with a Glu caused the Km and Ki values to increase significantly. In addition, the Kd values for Na+ or K+ were 5 to 8 fold higher. The negative charge of Asp-201 was shown to be vital for Na+ and K+ binding. Large amounts of Na+ or K+ had no effect on the very large Km and Ki values of D201N-β-galactosidase and the Vmax values changed minimally and in a linear rather than hyperbolic way. D201F-β-galactosidase, with a very bulky hydrophobic side chain in place of Asp, essentially obliterated all binding and catalysis.Key words: β-galactosidase, sodium, potassium, binding, aspartic acid.

scholarly journals mrp, a Multigene, Multifunctional Locus inBacillus subtilis with Roles in Resistance to Cholate and to Na+ and in pH Homeostasis

1999 ◽  
Vol 181 (8) ◽  
pp. 2394-2402 ◽  
Author(s):  
Masahiro Ito ◽  
Arthur A. Guffanti ◽  
Bauke Oudega ◽  
Terry A. Krulwich
Keyword(s):  
Double Mutant ◽  
Ph Regulation ◽  
Inducible Promoter ◽  
Cytoplasmic Ph ◽  
Null Mutant ◽  
Wild Type ◽  
Ph Homeostasis ◽  
In The Wild ◽  
Single Transcript ◽  
Membrane Spanning

ABSTRACT A 5.9-kb region of the Bacillus subtilis chromosome is transcribed as a single transcript that is predicted to encode seven membrane-spanning proteins. Homologues of the first gene of this operon, for which the designation mrp (multiple resistance and pH adaptation) is proposed here, have been suggested to encode an Na+/H+ antiporter or a K+/H+ antiporter. In the present studies of theB. subtilis mrp operon, both polar and nonpolar mutations in mrpA were generated. Growth of these mutants was completely inhibited by concentrations of added Na+ as low as 0.3 M at pH 7.0 and 0.03 M at pH 8.3; there was no comparable inhibition by added K+. A null mutant that was constructed by full replacement of the mrp operon was even more Na+ sensitive. A double mutant with mutations in both mrpA and the multifunctional antiporter-encodingtetA(L) gene was no more sensitive than themrpA mutants to Na+, consistent with a major role for mrpA in Na+ resistance. Expression of mrpA from an inducible promoter, upon insertion into the amyE locus, restored significant Na+ resistance in both the polar and nonpolarmrpA mutants but did not restore resistance in the null mutant. The mrpA disruption also resulted in an impairment of cytoplasmic pH regulation upon a sudden shift in external pH from 7.5 to 8.5 in the presence of Na+ and, to some extent, K+ in the range from 10 to 25 mM. By contrast, themrpA tetA(L) double mutant, like the tetA(L) single mutant, completely lost its capacity for both Na+- and K+-dependent cytoplasmic pH regulation upon this kind of shift at cation concentrations ranging from 10 to 100 mM; thus, tetA(L) has a more pronounced involvement thanmrpA in pH regulation. Measurements of Na+efflux from the wild-type strain, the nonpolar mrpA mutant, and the complemented mutant indicated that inducible expression ofmrpA increased the rate of protonophore- and cyanide-sensitive Na+ efflux over that in the wild-type in cells preloaded with 5 mM Na+. The mrpA and null mutants showed no such efflux in that concentration range. This is consistent with MrpA encoding a secondary, proton motive force-energized Na+/H+ antiporter. Studies of a polar mutant that leads to loss of mrpFG and its complementation in trans by mrpF ormrpFG support a role for MrpF as an efflux system for Na+ and cholate. Part of the Na+ efflux capacity of the whole mrp operon products is attributable to mrpF. Neither mrpF nor mrpFGexpression in trans enhanced the cholate or Na+resistance of the null mutant. Thus, one or more other mrpgene products must be present, but not at stoichiometric levels, for stability, assembly, or function of both MrpF and MrpA expressed intrans. Also, phenotypic differences among themrp mutants suggest that functions in addition to Na+ and cholate resistance and pH homeostasis will be found among the remaining mrp genes.

A Mutation That Improves Soluble Recombinant Hemoglobin Accumulation in Escherichia coli in Heme Excess

1999 ◽  
Vol 65 (2) ◽  
pp. 640-647 ◽  
Author(s):  
Michael J. Weickert ◽  
Maria Pagratis ◽  
Christopher B. Glascock ◽  
Richard Blackmore
Keyword(s):  
Escherichia Coli ◽  
Binding Pocket ◽  
Culture Conditions ◽  
Molar Ratio ◽  
Cell Protein ◽  
Wild Type ◽  
E Coli ◽  
Soluble Cell ◽  
Hemoglobin Variants ◽  
High Level

ABSTRACT High-level expression of soluble recombinant human hemoglobin (rHb) in Escherichia coli was obtained with several hemoglobin variants. Under identical conditions, two rHbs containing the Presbyterian mutation (Asn-108→Lys) in β-globin accumulated to approximately twofold less soluble globin than rHbs containing the corresponding wild-type β-globin subunit accumulated. The β-globin Providence(asp) mutation (Lys-82→Asp) significantly improved soluble rHb accumulation compared to the wild-type β-globin subunit and restored soluble accumulation of rHbs containing the Presbyterian mutation to wild-type levels. The Providenceasp substitution introduced a negatively charged residue into the normally cationic 2,3-bisphosphoglycerate binding pocket, potentially reducing the electrostatic repulsion in the absence of the polyanion. The average soluble globin accumulation when there was coexpression of di-α-globin and β-Lys-82→Asp-globin (rHb9.1) and heme was present in at least a threefold molar excess was 36% ± 3% of the soluble cell protein in E. coli. The average total accumulation (soluble globin plus insoluble globin) was 56% ± 7% of the soluble cell protein. Fermentations yielded 6.0 ± 0.3 g of soluble rHb9.1 per liter 16 h after induction and 6.4 ± 0.2 g/liter 24 h after induction. The average total globin yield was 9.4 g/liter 16 h after induction. High-level accumulation of soluble rHb in E. coli depends on culture conditions, the protein sequence, and the molar ratio of the heme cofactor added.

scholarly journals Engineering Candida tenuis Xylose Reductase for Improved Utilization of NADH: Antagonistic Effects of Multiple Side Chain Replacements and Performance of Site-Directed Mutants under Simulated In Vivo Conditions

2005 ◽  
Vol 71 (10) ◽  
pp. 6390-6393 ◽  
Author(s):  
Barbara Petschacher ◽  
Bernd Nidetzky
Keyword(s):  
Xylose Reductase ◽  
Binding Pocket ◽  
Kinetic Mechanism ◽  
Side Chain ◽  
Multiple Site ◽  
Wild Type ◽  
Structural Effects ◽  
Phosphate Binding ◽  
And Performance

ABSTRACT Six single- and multiple-site variants of Candida tenuis xylose reductase that were engineered to have side chain replacements in the coenzyme 2′-phosphate binding pocket were tested for NADPH versus NADH selectivity (R sel) in the presence of physiological reactant concentrations. The experimental R sel values agreed well with predictions from a kinetic mechanism describing mixed alternative coenzyme utilization. The Lys-274→Arg and Arg-280→His substitutions, which individually improved wild-type R sel 50- and 20-fold, respectively, had opposing structural effects when they were combined in a double mutant.

scholarly journals A Conserved Glycine Residue of Trimeric Autotransporter Domains Plays a Key Role in Yersinia Adhesin A Autotransport

2007 ◽  
Vol 189 (24) ◽  
pp. 9011-9019 ◽  
Author(s):  
Ulrike Grosskinsky ◽  
Monika Schütz ◽  
Michaela Fritz ◽  
Yvonne Schmid ◽  
Marina C. Lamparter ◽  
...  
Keyword(s):  
Host Cells ◽  
Side Chain ◽  
Wild Type ◽  
Membrane Pore ◽  
E Coli ◽  
Glycine Residue ◽  
Trimeric Autotransporter Adhesin ◽  
The Stability ◽  
Cell Cytokine Production

ABSTRACT The Yersinia adhesin A (YadA) is a trimeric autotransporter adhesin of enteric yersiniae. It consists of three major domains: a head mediating adherence to host cells, a stalk involved in serum resistance, and an anchor that forms a membrane pore and is responsible for the autotransport function. The anchor contains a glycine residue, nearly invariant throughout trimeric autotransporter adhesins, that faces the pore lumen. To address the role of this glycine, we replaced it with polar amino acids of increasing side chain size and expressed wild-type and mutant YadA in Escherichia coli. The mutations did not impair the YadA-mediated adhesion to collagen and to host cells or the host cell cytokine production, but they decreased the expression levels and stability of YadA trimers with increasing side chain size. Likewise, autoagglutination and resistance to serum were decreased in these mutants. We found that the periplasmic protease DegP is involved in the degradation of YadA and that in an E. coli degP deletion strain, mutant versions of YadA were expressed almost to wild-type levels. We conclude that the conserved glycine residue affects both the export and the stability of YadA and consequently some of its putative functions in pathogenesis.

scholarly journals Indole Pulse Signalling Regulates the Cytoplasmic pH ofE. coliin a Memory-Like Manner

2018 ◽  
Author(s):  
Ashraf Zarkan ◽  
Santiago Caño Muñiz ◽  
Jinbo Zhu ◽  
Kareem Al Nahas ◽  
Jehangir Cama ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Ph Regulation ◽  
Critical Role ◽  
Bacterial Cells ◽  
Cytoplasmic Ph ◽  
E Coli ◽  
Degree Of Protection ◽  
Bacterial Cell Membrane ◽  
Ph Range ◽  
Phase Entry

SUMMARYBacterial cells are critically dependent upon pH regulation. Most proteins function over a limited pH range and the pH gradient across the bacterial cell membrane is central to energy production and transduction1. Here we demonstrate that indole plays a critical role in the regulation of the cytoplasmic pH ofE. coli. Indole is an aromatic molecule with diverse signalling roles that in bacteria is produced from tryptophan by the enzyme tryptophanase (TnaA)2. Two modes of indole signalling have been described: persistent and pulse signalling. The latter is illustrated by the brief but intense elevation of intracellular indole during stationary phase entry3,4. We show thatE. colicells growing under conditions where no indole is produced maintain their cytoplasmic pH at 7.8 ± 0.2. In contrast, under conditions permitting indole production, pH is maintained at 7.2 ± 0.2. Experiments where indole was added experimentally to non-producing cultures showed that pH regulation results from pulse, rather than persistent, indole signalling. Furthermore, the application of an artificial pulse of either of two non-biological proton ionophores (DNP or CCCP) caused a similar effect, suggesting that the relevant property of indole in this context is its ability to conduct protons across the cytoplasmic membrane5. Additionally, we show that the effect of the indole pulse that occurs normally during stationary phase entry in rich medium remains as a “memory” to maintain the correct cytoplasmic pH until entry into the next stationary phase. The indole-mediated reduction in cytoplasmic pH may explain why indole providesE. coliwith a degree of protection against stresses, including some bactericidal antibiotics.

scholarly journals New Pathogenic Thyrotropin Receptor Mutations Decipher Differentiated Activity Switching at a Conserved Helix 6 Motif of Family A GPCR

2012 ◽  
Vol 97 (2) ◽  
pp. E228-E232 ◽  
Author(s):  
Heike Biebermann ◽  
Franziska Winkler ◽  
Daniela Handke ◽  
Anke Teichmann ◽  
Burkhard Gerling ◽  
...  
Keyword(s):  
Transmembrane Helix ◽  
Helical Conformation ◽  
Side Chain ◽  
Wild Type ◽  
Pathogenic Mechanisms ◽  
Activating Mutations ◽  
Naturally Occurring ◽  
High Conservation ◽  
Inactivating Mutation ◽  
G Protein Coupled

Context: In this paper we report two new TSH receptor (TSHR) mutations. One mutation (Pro6396.50Leu) was identified in two siblings with congenital hypothyroidism, and a second mutation (Cys6366.47Arg) was found in a patient suffering from nonautoimmune hyperthyroidism. Both mutations are located in transmembrane helix (TMH) 6 at the conserved Cys6.47-Trp(Met)6.48-Leu(Ala)6.49-Pro6.50 motif of family A G protein-coupled receptors (GPCR). Objective: To study the pathogenic mechanisms, we tested patients' mutations and further side chain variations regarding their effects on TSHR signaling. Results: Substitution Pro639Leu fully inactivates the promiscuous TSHR for cAMP (Gs) and IP (Gq) signaling. In contrast, Cys636Arg leads to constitutive activation of Gs. Organization of TSHR in oligomers was not modified by mutations at position 636. Interestingly, it is known from crystal structures of GPCR that Pro6.50 is located at a TMH6 kink-distortion, which is a pivot during activation-related helical movements. However, the cell surface expressions of all mutants at position 639 were comparable to wild type, indicating a helical conformation like wild type. Conclusion: Until now, only naturally occurring constitutively activating mutations in TSHR TMH6 have been reported, but here we present the first pathogenic inactivating mutation (Pro639Leu). Our data are indicative of differentiated regulation of Gs and Gq signaling at particular TMH6 positions, but without any effects on TSHR oligomer constellation. Details of signaling modulation by each mutant at positions 6366.47 and 6396.50 help us to understand high conservation of these amino acids in family A GPCR. Described molecular (pathogenic) mechanisms are likely not unique for TSHR.

scholarly journals Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alina Ornik-Cha ◽  
Julia Wilhelm ◽  
Jessica Kobylka ◽  
Hanno Sjuts ◽  
Attilio V. Vargiu ◽  
...  
Keyword(s):  
Efflux Pump ◽  
Efflux Pumps ◽  
Binding Pocket ◽  
Drug Binding ◽  
Side Chain ◽  
E Coli ◽  
Cryo Electron Microscopy ◽  
Antibiotic Compounds ◽  
Periplasmic Domain ◽  
Transport Channels

AbstractUpon antibiotic stress Gram-negative pathogens deploy resistance-nodulation-cell division-type tripartite efflux pumps. These include a H+/drug antiporter module that recognizes structurally diverse substances, including antibiotics. Here, we show the 3.5 Å structure of subunit AdeB from the Acinetobacter baumannii AdeABC efflux pump solved by single-particle cryo-electron microscopy. The AdeB trimer adopts mainly a resting state with all protomers in a conformation devoid of transport channels or antibiotic binding sites. However, 10% of the protomers adopt a state where three transport channels lead to the closed substrate (deep) binding pocket. A comparison between drug binding of AdeB and Escherichia coli AcrB is made via activity analysis of 20 AdeB variants, selected on basis of side chain interactions with antibiotics observed in the AcrB periplasmic domain X-ray co-structures with fusidic acid (2.3 Å), doxycycline (2.1 Å) and levofloxacin (2.7 Å). AdeABC, compared to AcrAB-TolC, confers higher resistance to E. coli towards polyaromatic compounds and lower resistance towards antibiotic compounds.

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