Studies on the X-Ray and Solution Structure of FeoB from Escherichia coli BL21

Hagelueken, Gregor; Hoffmann, Jan; Schubert, E.; Duthie, F.G.; Florin, Nicole; Konrad, Lisa; Imhof, Diana; Behrmann, Elmar; Morgner, Nina; Schiemann, Olav

doi:10.1016/j.bpj.2016.05.018

Cited by 18 publications

(12 citation statements)

References 39 publications

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“…The metal transporters from Escherichia coli strain F11 (ID: 3NRP) and NFeoB from Escherichia coli BL21 (ID: 5FH9) which are of importance to iron metabolism of many bacteria [21,22] were downloaded from protein data bank. The molecular docking simulation was used to investigate the interactions of the phytochemicals with the Escherichia coli receptors.…”

Section: Computational Detailsmentioning

confidence: 99%

Phytochemical Profile, Antioxidant Activity of Leaf of Hoslundia opposita Vahl and Docking of its Phytochemical Components with Uropathogenic Strain F11(ID:3NRP) and NFeoB from Escherichia coli BL21(ID:5FH9)

Edewor

Ogundola

Akintola

et al. 2021

AJRB

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Hoslundia opposita Vahl is a multi-purpose medicinal plant used traditionally to treat gonorrhea, cystitis, cough, fever, snake bites, convulsion in many parts of Africa. The objectives of this research are to evaluate the phytochemical profile, antioxidant activity of the leaves of Hoslundia opposita Vahl and to dock its phytochemical components with uropathogenic Escherichia coli strain F11(ID:3NRP) and NFeoB from Escherichia coli BL21(ID:5FH9). Harborne’s method was used for the identification of the class of phytochemicals while GC-MS was used to identify the type of phytochemicals. Folin-Ciocalteau method was used to determine the total phenolic content while aluminum colorimetric assay was used to estimate the total flavonoid content. 1, 1-diphenyl-2-picrylhydrazyl (DPPH) was used to evaluate the antioxidant activity. The molecular docking simulation method was used to investigate the interactions of the phytochemicals with the Escherichia coli receptors. In the phytochemical studies, flavonoids, terpenoids, cardiac glycosides and saponins were identified to be present in the methanolic leaf extract while steroids, alkaloids and anthraquinones were absent. The GC-MS analysis of the methanolic extract revealed presence of 17 compounds out of which 14 were identified. The compounds with appreciable quantity in the leaf extract were 1, 2, 3-benzetriol (38.11%), n-hexadacanoic acid (13.52%) and catechol (9.98%). Assessment of the antioxidant activity using DPPH gave a scavenging activity of 79.86% at 500ug/ml compared with ascorbic acid having a scavenging activity of 90.85% at the same concentration. Evaluation of the total phenolic and flavonoid contents at 500 ug/ml gave the values of 262.54 mg gallic acid equivalent/g extract and 6.24 mg quercetin equivalent/g extract respectively compared with gallic acid and quercetin with maximum concentrations of 385.12 and 12.46 respectively. This shows that the extract has significant antioxidant activity and can be explored as a valuable source of natural antioxidants. GC-MS analysis of the methanolic extract of Hoslundia opposita showed the presence of trans-3-(trifluoromethyl)cinnamic acid, octadecyl ester which was active against Escherichia coli. Docking results with 3NRP and 5FH9 showed binding affinities of -6.1, -6.6, 7.2and -7.0,7.4, 8.5 kJ/mol with the commercial drugs : ciprofloxacin, levofloxacin and tetracycline respectively while that of trans 3-(trifluoromethyl)cinnamic acid, octadecyl ester identified in the leaves were 5.6 and 5.9 kJ/mol.

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Section: Computational Detailsmentioning

confidence: 99%

Phytochemical Profile, Antioxidant Activity of Leaf of Hoslundia opposita Vahl and Docking of its Phytochemical Components with Uropathogenic Strain F11(ID:3NRP) and NFeoB from Escherichia coli BL21(ID:5FH9)

Edewor

Ogundola

Akintola

et al. 2021

AJRB

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“…Except for small single-domain globular proteins, one may need to test whether a crystal structure is representative of the solution structure. PDS-based distance distributions can provide this information [70], which is particularly useful when different techniques result in different predictions of solution structure [71] or when a shortened construct had to be used for crystallization [46,72].…”

Section: Integrative Modellingmentioning

confidence: 99%

The contribution of modern EPR to structural biology

Jeschke

2018

Emerging Topics in Life Sciences

111

133

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Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron-electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

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“…FeoB contains two domains, a cytoplasmic N-terminal domain that shows a GTPase activity, and a C-terminal domain that consists of transmembrane helices. The three-dimensional structure of E. coli FeoB N-terminal domain (PDB code 5FH9) [52] is showed in Fig. 3b-I.…”

Section: The Xanthomonas Citri Xss Clustermentioning

confidence: 99%

Genetic and structural determinants on iron assimilation pathways in the plant pathogen Xanthomonas citri subsp. citri and Xanthomonas sp.

Guerra

Balan

2020

Braz J Microbiol

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Iron is a vital nutrient to bacteria, not only in the basal metabolism but also for virulent species in infection and pathogenicity at their hosts. Despite its relevance, the role of iron in Xanthomonas citri infection, the etiological agent of citrus canker disease, is poorly understood in contrast to other pathogens, including other members of the Xanthomonas genus. In this review, we present iron assimilation pathways in X. citri including the ones for siderophore production and siderophore-iron assimilation, proven to be key factors to virulence in many organisms like Escherichia coli and Xanthomonas campestris. Based on classical iron-related proteins previously characterized in E. coli, Pseudomonas aeruginosa, and also Xanthomonadaceae, we identified orthologs in X. citri and evaluated their sequences, structural characteristics such as functional motifs, and residues that support their putative functions. Among the identified proteins are TonB-dependent receptors, periplasmic-binding proteins, active transporters, efflux pumps, and cytoplasmic enzymes. The role of each protein for the bacterium was analyzed and complemented with proteomics data previously reported. The global view of different aspects of iron regulation and nutrition in X. citri virulence and pathogenesis may help guide future investigations aiming the development of new drug targets against this important phytopathogen.

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Studies on the X-Ray and Solution Structure of FeoB from Escherichia coli BL21

Cited by 18 publications

References 39 publications

Phytochemical Profile, Antioxidant Activity of Leaf of Hoslundia opposita Vahl and Docking of its Phytochemical Components with Uropathogenic Strain F11(ID:3NRP) and NFeoB from Escherichia coli BL21(ID:5FH9)

Phytochemical Profile, Antioxidant Activity of Leaf of Hoslundia opposita Vahl and Docking of its Phytochemical Components with Uropathogenic Strain F11(ID:3NRP) and NFeoB from Escherichia coli BL21(ID:5FH9)

The contribution of modern EPR to structural biology

Genetic and structural determinants on iron assimilation pathways in the plant pathogen Xanthomonas citri subsp. citri and Xanthomonas sp.

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