scholarly journals The crystal structure of heme d1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo

2020 ◽  
Author(s):  
Thomas Klünemann ◽  
Steffi Henke ◽  
Wulf Blankenfeldt
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Opportunistic Pathogen ◽  
Nitrite Reduction ◽  
Asymmetric Unit ◽  
Maximum Resolution ◽  
High Protein Concentration ◽  
Domains Of Life ◽  
Sad Phasing ◽  
Heme D1

AbstractMonoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, we have determined the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa. Crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of eleven NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D-domain-swapped dimers, one showing pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison to similar proteins may offer new leads to unravel the unknown function of NirC.SynopsisThe crystal structure of the c-type cytochrome NirC from Pseudomonas aeruginosa has been determined and reveals the simultaneous presence of monomers and 3D-domain-swapped dimers in the same asymmetric unit.

scholarly journals The crystal structure of the heme d 1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo

2020 ◽  
Vol 76 (4) ◽  
pp. 375-384
Author(s):  
Thomas Klünemann ◽  
Steffi Henke ◽  
Wulf Blankenfeldt
Keyword(s):  
Crystal Structure ◽  
Protein Concentration ◽  
Opportunistic Pathogen ◽  
Nitrite Reduction ◽  
Simultaneous Observation ◽  
Maximum Resolution ◽  
High Protein Concentration ◽  
Different Types ◽  
Domains Of Life ◽  
Sad Phasing

Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa, has been determined. The crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution of 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of 11 NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D domain-swapped dimers, one of which shows pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between the high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison with similar proteins may offer new leads to unravel the unknown function of NirC.

scholarly journals Structure of heme d1-free cd1 nitrite reductase NirS

2020 ◽  
Author(s):  
Thomas Klünemann ◽  
Wulf Blankenfeldt
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Nitrite Reductase ◽  
Active Site ◽  
Opportunistic Pathogen ◽  
Free Form ◽  
Nitrate Respiration ◽  
Gram Negative ◽  
Open Conformation ◽  
Heme D1 ◽  
Insight Into

AbstractA key step in anaerobic nitrate respiration is the reduction of nitrite to nitric oxide, which is catalysed by cd1 nitrite reductase NirS in e.g. the gram-negative opportunistic pathogen Pseudomonas aeruginosa. Each subunit of this homodimeric enzyme consists of a cytochrome c domain and an eight-bladed β-propeller that binds the uncommon isobacteriochlorin heme d1 as an essential part of its active site. Although NirS is mechanistically and structurally well studied, the focus of previous studies has been on the active, heme d1-bound form. The heme d1-free form of NirS reported here, representing a premature state of the reductase, adopts an open conformation with the cytochrome c domains moved away from each other with respect to the active enzyme. Further, movement of a loop around W498 seems to be related to a widening of the propeller, allowing easier access to the heme d1 binding side. Finally, a possible link between the open conformation of NirS and flagella formation in P. aeruginosa is discussed.SynopsisThe crystal structure of heme d1-free cd1 nitrite reductase NirS from Pseudomonas aeruginosa has been determined and provides insight into a premature form of the enzyme.

Crystal Structure of Dihydro-Heme d1 Dehydrogenase NirN from Pseudomonas aeruginosa Reveals Amino Acid Residues Essential for Catalysis

2019 ◽  
Vol 431 (17) ◽  
pp. 3246-3260 ◽  
Author(s):  
Thomas Klünemann ◽  
Arne Preuß ◽  
Julia Adamczack ◽  
Luis F.M. Rosa ◽  
Falk Harnisch ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Residues ◽  
Heme D1

The In Vitro Antibiofilm Activity of Water Leaf Extract of Papaya (Carica papaya L.) against Pseudomonas aeruginosa

2017 ◽  
Vol 2 (3) ◽  
pp. 150-163
Author(s):  
Ekajayanti Kining ◽  
Syamsul Falah ◽  
Novik Nurhidayat
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Contact Time ◽  
Cell Attachment ◽  
Water Extract ◽  
Opportunistic Pathogen ◽  
Bacterial Biofilm ◽  
Antibiofilm Activity ◽  
Bacterial Survival ◽  
Optimum Conditions

Pseudomonas aeruginosa is one of opportunistic pathogen forming bacterial biofilm. The biofilm sustains the bacterial survival and infections. This study aimed to assess the activity of water extract of papaya leaves on inhibition of cells attachment, growth and degradation of the biofilm using crystal violet (CV) biofilm assay. Research results showed that water extract of papaya leaves contains alkaloids, tanins, flavonoids, and steroids/terpenoids and showed antibacterial activity and antibiofilm against P. aeruginosa. Addition of extract can inhibit the cell attachment and was able to degrade the biofilm of 40.92% and 48.058% respectively at optimum conditions: extract concentration of 25% (v/v), temperature 37.5 °C and contact time 45 minutes. With a concentration of 25% (v/v), temperature of 50 °C and the contact time of 3 days, extract of papaya leaves can inhibit the growth of biofilms of 39.837% v/v.

Alkyl-chain disorder in tetraisohexylammonium bromide

2012 ◽  
Vol 68 (4) ◽  
pp. o152-o155 ◽  
Author(s):  
Malcolm A. Kelland ◽  
Amber L. Thompson
Keyword(s):  
Crystal Structure ◽  
Crystal Growth ◽  
Alkyl Chain ◽  
Growth Inhibitor ◽  
Ammonium Cation ◽  
Asymmetric Unit ◽  
Bromide Anion ◽  
Alkyl Chains ◽  
Hydrate Crystal ◽  
Structure Ii Clathrate Hydrate

Tetraisohexylammonium bromide [systematic name: tetrakis(4-methylpentyl)azanium bromide], C24H52N+·Br−, is a powerful structure II clathrate hydrate crystal-growth inhibitor. The crystal structure, in the space groupP3221, contains one ammonium cation and one bromide anion in the asymmetric unit, both on general positions. At 100 K, the ammonium cation exhibits one ordered isohexyl chain and three disordered isohexyl chains. At 250 K, all four isohexyl chains are disordered. In an effort to reduce the disorder in the alkyl chains, the crystal was thermally cycled, but the disorder remained, indicating that it is dynamic in nature.

2,4-Diamino-6-phenyl-1,3,5-triazin-1-ium nitrate: intriguing crystal structure with high Z′/Z′′ and hydrogen bond numbers and Hirshfeld surface analysis of intermolecular interactions

CrystEngComm ◽  
2021 ◽  
Author(s):  
Nicoleta Caimac ◽  
Elena Melnic ◽  
Diana Chisca ◽  
Marina S. Fonari
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Surface Analysis ◽  
Intermolecular Interactions ◽  
Title Compound ◽  
Ionic Species ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Asymmetric Unit ◽  
Space Group

The title compound crystallises in the triclinic centrosymmetric space group P1̄ with an intriguing high number of crystallographically unique binary salt-like adducts (Z′ = 8) and a total number of ionic species (Z′′ = 16) in the asymmetric unit.

scholarly journals Prevalence of metallo-β-lactamase genes among Pseudomonas aeruginosa isolated from various clinical samples in China

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Wei Wang ◽  
Xiaoya Wang
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Susceptibility ◽  
Ethylenediaminetetraacetic Acid ◽  
Carbapenem Resistance ◽  
Opportunistic Pathogen ◽  
Detection Methods ◽  
Clinical Samples ◽  
Routine Practice ◽  
Carbapenem Resistant ◽  
High Prevalence

AbstractBackgroundPseudomonas aeruginosa is an opportunistic pathogen which is associated with nosocomial infections and causes various diseases including urinary tract infection, pneumonia, soft-tissue infection and sepsis. The emergence of P. aeruginosa-acquired metallo-β-lactamase (MBL) is most worrisome and poses a serious threat during treatment and infection control. The objective of this study was to identify antibiotic susceptibility, phenotypic detection of MBL production and to determine the prevalence of MBL genes in carbapenem-resistant P. aeruginosa isolated from different clinical samples.MethodsA total of 329 non-duplicate P. aeruginosa isolated from various clinical samples from two hospitals in China between September 2017 and March 2019 were included in this study. Phenotypic detection of MBL was performed by the combined detection method using imipenem and imipenem-ethylenediaminetetraacetic acid (EDTA) discs. MBL-encoding genes including blaVIM-1, blaVIM-2, blaIMP-1, blaIMP-2, blaSPM-1, blaSIM, blaNDM-1 and blaGIM were detected by polymerase chain reaction (PCR).ResultsOf the 329 P. aeruginosa, majority of the isolates were resistant to imipenem (77.5%) followed by meropenem (64.7%). Of the 270 P. aeruginosa isolates tested, 149 (55.2%) isolates were found to be positive for MBL detection. Of the different samples, 57.8% (n = 26) of P. aeruginosa isolated from blood were found to be positive for MBL production. Of the various MBL genes, blaIMP-1 (28.2%) was the most predominant gene detected followed by blaVIM-2 (18.8%), blaVIM-1 (16.1%), blaNDM-1 (9.4%), blaIMP-2 (6.7%), blaSIM (6.0%), blaSPM-1 (4.0%) and blaGIM (1.3%) genes.ConclusionsThe high resistance of P. aeruginosa toward imipenem and meropenem and the high prevalence of blaIMP-1 and blaVIM-2 set the alarm on the increasing, perhaps the increased, carbapenem resistance. In addition to routine antibiotic susceptibility testings, our results emphasize the importance of both the phenotypic and genotypic MBL detection methods in routine practice for early detection of carbapenem resistance and to prevent further dissemination of this resistant pathogen.

scholarly journals Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

2008 ◽  
Vol 190 (8) ◽  
pp. 2790-2803 ◽  
Author(s):  
Matthew A. Oberhardt ◽  
Jacek Puchałka ◽  
Kimberly E. Fryer ◽  
Vítor A. P. Martins dos Santos ◽  
Jason A. Papin
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Metabolic Network ◽  
Opportunistic Pathogen ◽  
Scale Model ◽  
Modeling Framework ◽  
Major Life ◽  
Metabolic Versatility ◽  
A Genome ◽  
Scale Properties ◽  
Genome Scale

ABSTRACT Pseudomonas aeruginosa is a major life-threatening opportunistic pathogen that commonly infects immunocompromised patients. This bacterium owes its success as a pathogen largely to its metabolic versatility and flexibility. A thorough understanding of P. aeruginosa's metabolism is thus pivotal for the design of effective intervention strategies. Here we aim to provide, through systems analysis, a basis for the characterization of the genome-scale properties of this pathogen's versatile metabolic network. To this end, we reconstructed a genome-scale metabolic network of Pseudomonas aeruginosa PAO1. This reconstruction accounts for 1,056 genes (19% of the genome), 1,030 proteins, and 883 reactions. Flux balance analysis was used to identify key features of P. aeruginosa metabolism, such as growth yield, under defined conditions and with defined knowledge gaps within the network. BIOLOG substrate oxidation data were used in model expansion, and a genome-scale transposon knockout set was compared against in silico knockout predictions to validate the model. Ultimately, this genome-scale model provides a basic modeling framework with which to explore the metabolism of P. aeruginosa in the context of its environmental and genetic constraints, thereby contributing to a more thorough understanding of the genotype-phenotype relationships in this resourceful and dangerous pathogen.

scholarly journals Control of a programmed cell death pathway in Pseudomonas aeruginosa by an antiterminator

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jennifer M. Peña ◽  
Samantha M. Prezioso ◽  
Kirsty A. McFarland ◽  
Tracy K. Kambara ◽  
Kathryn M. Ramsey ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Dna Damage ◽  
Cell Death ◽  
Programmed Cell Death ◽  
Rna Polymerase ◽  
Virulence Genes ◽  
Opportunistic Pathogen ◽  
Transcription Activator ◽  
Present Evidence ◽  
Cell Death Pathway

AbstractIn Pseudomonas aeruginosa the alp system encodes a programmed cell death pathway that is switched on in a subset of cells in response to DNA damage and is linked to the virulence of the organism. Here we show that the central regulator of this pathway, AlpA, exerts its effects by acting as an antiterminator rather than a transcription activator. In particular, we present evidence that AlpA positively regulates the alpBCDE cell lysis genes, as well as genes in a second newly identified target locus, by recognizing specific DNA sites within the promoter, then binding RNA polymerase directly and allowing it to bypass intrinsic terminators positioned downstream. AlpA thus functions in a mechanistically unusual manner to control the expression of virulence genes in this opportunistic pathogen.

scholarly journals Powder study of 3-azabicyclo[3.3.1]nonane-2,4-dione form 2

2006 ◽  
Vol 62 (7) ◽  
pp. o3046-o3048 ◽  
Author(s):  
Ashley T Hulme ◽  
Philippe Fernandes ◽  
Alastair Florence ◽  
Andrea Johnston ◽  
Kenneth Shankland
Keyword(s):  
Crystal Structure ◽  
Simulated Annealing ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Title Compound ◽  
Variable Temperature ◽  
Polycrystalline Sample ◽  
Asymmetric Unit ◽  
X Ray ◽  
Compound C

A polycrystalline sample of a new polymorph of the title compound, C8H11NO2, was produced during a variable-temperature X-ray powder diffraction study. The crystal structure was solved at 1.67 Å resolution by simulated annealing from laboratory powder data collected at 250 K. Subsequent Rietveld refinement yielded an R wp of 0.070 to 1.54 Å resolution. The structure contains two molecules in the asymmetric unit, which form a C 2 2(8) chain motif via N—H...O hydrogen bonds.

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