scholarly journals Structural studies of the unusual metal-ion site of the GH124 endoglucanase from Ruminiclostridium thermocellum

2018 ◽  
Vol 74 (8) ◽  
pp. 496-505 ◽  
Author(s):  
Saioa Urresti ◽  
Alan Cartmell ◽  
Feng Liu ◽  
Paul H. Walton ◽  
Gideon J. Davies
Keyword(s):  
Transition Metal ◽  
Metal Binding ◽  
Metal Ion ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Biomass Degradation ◽  
Carbohydrate Active Enzymes ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases ◽  
The Many

The recent discovery of `lytic' polysaccharide monooxygenases, copper-dependent enzymes for biomass degradation, has provided new impetus for the analysis of unusual metal-ion sites in carbohydrate-active enzymes. In this context, the CAZY family GH124 endoglucanase from Ruminiclostridium thermocellum contains an unusual metal-ion site, which was originally modelled as a Ca2+ site but features aspartic acid, asparagine and two histidine imidazoles as coordinating residues, which are more consistent with a transition-metal binding environment. It was sought to analyse whether the GH124 metal-ion site might accommodate other metals. It is demonstrated through thermal unfolding experiments that this metal-ion site can accommodate a range of transition metals (Fe2+, Cu2+, Mn2+ and Ni2+), whilst the three-dimensional structure and mass spectrometry show that one of the histidines is partially covalently modified and is present as a 2-oxohistidine residue; a feature that is rarely observed but that is believed to be involved in an `off-switch' to transition-metal binding. Atomic resolution (<1.1 Å) complexes define the metal-ion site and also reveal the binding of an unusual fructosylated oligosaccharide, which was presumably present as a contaminant in the cellohexaose used for crystallization. Although it has not been possible to detect a biological role for the unusual metal-ion site, this work highlights the need to study some of the many metal-ion sites in carbohydrate-active enzymes that have long been overlooked or previously mis-assigned.

scholarly journals Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172

2020 ◽  
Author(s):  
Monika Tõlgo ◽  
Silvia Hüttner ◽  
Nguyen Than Thuy ◽  
Vu Nguyen Than ◽  
Johan Larsbrink ◽  
...  
Keyword(s):  
Gc Content ◽  
Low Ph ◽  
Biomass Degradation ◽  
Carbohydrate Active Enzymes ◽  
Thielavia Terrestris ◽  
Biomass Saccharification ◽  
Lignocellulosic Substrates ◽  
Lytic Polysaccharide Monooxygenases ◽  
Beechwood Xylan ◽  
Polysaccharide Monooxygenases

Abstract Background: Biomass-degrading enzymes with improved activity and stability can ameliorate substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate well low pH and high temperatures. Here, we aimed to illuminate the lignocellulose degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail.Results: We sequenced and analysed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. In total, 411 CAZy domains were found among 10,128 predicted genes. Compared to other fungi, auxiliary activity (AA) enzymes were particularly enriched. GC content was higher in coding sequences than in the overall genome. A high GC3 content was hypothesised to contribute to thermophilicity. T. terrestris employed mainly lytic polysaccharide monooxygenases (LPMOs) and glycoside hydrolase (GH) family 7 glucanases to attack cellulosic substrates, and conventional hemicellulases (GH10 and GH11) to degrade xylan. The observed co-expression and co-upregulation of AA9 LPMOs, other AA CAZymes, and (hemi)cellulases points to a complex and nuanced degradation strategy. Growth on more complex and heterogeneous substrates resulted in a more varied but generally lower gene expression. Conclusions: Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterisation of potential new enzymes for industrial biomass saccharification.

scholarly journals PilB from Streptococcus sanguinis is a bimodular type IV pilin with a direct role in adhesion

2021 ◽  
Vol 118 (22) ◽  
pp. e2102092118
Author(s):  
Claire Raynaud ◽  
Devon Sheppard ◽  
Jamie-Lee Berry ◽  
Ishwori Gurung ◽  
Vladimir Pelicic
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Functional Module ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Direct Role ◽  
Streptococcus Sanguinis ◽  
Type Iv ◽  
Type Iv Pilin ◽  
Von Willebrand

Type IV pili (T4P) are functionally versatile filamentous nanomachines, nearly ubiquitous in prokaryotes. They are predominantly polymers of one major pilin but also contain minor pilins whose functions are often poorly defined and likely to be diverse. Here, we show that the minor pilin PilB from the T4P of Streptococcus sanguinis displays an unusual bimodular three-dimensional structure with a bulky von Willebrand factor A–like (vWA) module “grafted” onto a small pilin module via a short loop. Structural modeling suggests that PilB is only compatible with a localization at the tip of T4P. By performing a detailed functional analysis, we found that 1) the vWA module contains a canonical metal ion–dependent adhesion site, preferentially binding Mg2+ and Mn2+, 2) abolishing metal binding has no impact on the structure of PilB or piliation, 3) metal binding is important for S. sanguinis T4P–mediated twitching motility and adhesion to eukaryotic cells, and 4) the vWA module shows an intrinsic binding ability to several host proteins. These findings reveal an elegant yet simple evolutionary tinkering strategy to increase T4P functional versatility by grafting a functional module onto a pilin for presentation by the filaments. This strategy appears to have been extensively used by bacteria, in which modular pilins are widespread and exhibit an astonishing variety of architectures.

scholarly journals Antibodies against Thrombospondin-Related Anonymous Protein Do Not Inhibit Plasmodium Sporozoite Infectivity In Vivo

2000 ◽  
Vol 68 (6) ◽  
pp. 3667-3673 ◽  
Author(s):  
Soren Gantt ◽  
Cathrine Persson ◽  
Keith Rose ◽  
Ashley J. Birkett ◽  
Ruben Abagyan ◽  
...  
Keyword(s):  
Metal Ion ◽  
Competitive Inhibition ◽  
Polyclonal Antibodies ◽  
Three Dimensional ◽  
Calcium Ionophore ◽  
Plasmodium Yoelii ◽  
Gliding Motility ◽  
Vaccine Antigen ◽  
Dimensional Structure

ABSTRACT Thrombospondin-related anonymous protein (TRAP), a candidate malaria vaccine antigen, is required for Plasmodiumsporozoite gliding motility and cell invasion. For the first time, the ability of antibodies against TRAP to inhibit sporozoite infectivity in vivo is evaluated in detail. TRAP contains an A-domain, a well-characterized adhesive motif found in integrins. We modeled here a three-dimensional structure of the TRAP A-domain of Plasmodium yoelii and located regions surrounding the MIDAS (metal ion-dependent adhesion site), the presumed business end of the domain. Mice were immunized with constructs containing these A-domain regions but were not protected from sporozoite challenge. Furthermore, monoclonal and rabbit polyclonal antibodies against the A-domain, the conserved N terminus, and the repeat region of TRAP had no effect on the gliding motility or sporozoite infectivity to mice. TRAP is located in micronemes, secretory organelles of apicomplexan parasites. Accordingly, the antibodies tested here stained cytoplasmic TRAP brightly by immunofluorescence. However, very little TRAP could be detected on the surface of sporozoites. In contrast, a dramatic relocalization of TRAP onto the parasite surface occurred when sporozoites were treated with calcium ionophore. This likely mimics the release of TRAP from micronemes when a sporozoite contacts its target cell in vivo. Contact with hepatoma cells in culture also appeared to induce the release of TRAP onto the surface of sporozoites. If large amounts of TRAP are released in close proximity to its cellular receptor(s), effective competitive inhibition by antibodies may be difficult to achieve.

TonB or not TonB: is that the question?This paper is one of a selection of papers published in a Special Issue entitled CSBMCB 53rd Annual Meeting — Membrane Proteins in Health and Disease, and has undergone the Journal’s usual peer review process.

2011 ◽  
Vol 89 (2) ◽  
pp. 87-97 ◽  
Author(s):  
Karla D. Krewulak ◽  
Hans J. Vogel
Keyword(s):  
Outer Membrane ◽  
Metal Ion ◽  
Peer Review Process ◽  
Three Dimensional ◽  
Membrane Receptor ◽  
Membrane Receptors ◽  
Dimensional Structure ◽  
Outer Membrane Receptor ◽  
Different Strains ◽  
Low Molecular Weight Iron

Bacteria are able to survive in low-iron environments by sequestering this metal ion from iron-containing proteins and other biomolecules such as transferrin, lactoferrin, heme, hemoglobin, or other heme-containing proteins. In addition, many bacteria secrete specific low molecular weight iron chelators termed siderophores. These iron sources are transported into the Gram-negative bacterial cell through an outer membrane receptor, a periplasmic binding protein (PBP), and an inner membrane ATP-binding cassette (ABC) transporter. In different strains the outer membrane receptors can bind and transport ferric siderophores, heme, or Fe3+ as well as vitamin B12, nickel complexes, and carbohydrates. The energy that is required for the active transport of these substrates through the outer membrane receptor is provided by the TonB/ExbB/ExbD complex, which is located in the cytoplasmic membrane. In this minireview, we will briefly examine the three-dimensional structure of TonB and the current models for the mechanism of TonB-dependent energy transduction. Additionally, the role of TonB in colicin transport will be discussed.

Metal Ion-Driven Assembly of Two New Coordination Polymers Constructed by Asymmetric Tricarboxylate and Imidazole-Containing Ligands: Syntheses, Crystal Structures, and Luminescent Properties

2015 ◽  
Vol 68 (1) ◽  
pp. 121 ◽  
Author(s):  
Wenlong Liu ◽  
Xueying Wang ◽  
Mengqiang Wu ◽  
Bing Wang
Keyword(s):  
Infrared Spectroscopy ◽  
Coordination Polymers ◽  
Metal Ion ◽  
Three Dimensional ◽  
Luminescent Properties ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Dimethyl Benzene

Two new coordination polymers, namely, {[Cd3(bpt)2(bimb)2]·2(H2O)}n (1) and [Zn3(bpt)2(bimb)2]n (2) (bpt = biphenyl-3,4′,5-tricarboxylate, bimb = 1,4-bis(1-imidazol-yl)-2,5-dimethyl benzene), have been obtained under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analysis and further characterised by elemental analysis and infrared spectroscopy. Complex 1 exhibits a trinodal (4,4,4)-connected topology with Schläfli symbol of (4.62.83)4.(64.82). Complex 2 is also a three-dimensional structure and displays a (3,4,6)-connected topology with Schläfli symbol of (4.62)2.(42.66.85.102).(64.82). It is shown that the asymmetrically tricarboxylate can bear diverse structures regulated by metal ions. The photoluminescence behaviours of compounds 1 and 2 were also discussed.

scholarly journals The three-dimensional structure of the cellobiohydrolase Cel7A fromAspergillus fumigatusat 1.5 Å resolution

2015 ◽  
Vol 71 (1) ◽  
pp. 114-120 ◽  
Author(s):  
Olga V. Moroz ◽  
Michelle Maranta ◽  
Tarana Shaghasi ◽  
Paul V. Harris ◽  
Keith S. Wilson ◽  
...  
Keyword(s):  
Enzymatic Degradation ◽  
Plant Cell Wall ◽  
Three Dimensional ◽  
Biofuel Production ◽  
Industrial Processes ◽  
Dimensional Structure ◽  
Carbohydrate Active Enzymes ◽  
Cazy Database ◽  
Generation Biofuel ◽  
Insight Into

The enzymatic degradation of plant cell-wall cellulose is central to many industrial processes, including second-generation biofuel production. Key players in this deconstruction are the fungal cellobiohydrolases (CBHs), notably those from family GH7 of the carbohydrate-active enzymes (CAZY) database, which are generally known as CBHI enzymes. Here, three-dimensional structures are reported of theAspergillus fumigatusCBHI Cel7A solved in uncomplexed and disaccharide-bound forms at resolutions of 1.8 and 1.5 Å, respectively. The product complex with a disaccharide in the +1 and +2 subsites adds to the growing three-dimensional insight into this family of industrially relevant biocatalysts.

scholarly journals The many faces of amyloid: Protein misfolding: failure or function?

2011 ◽  
Vol 33 (5) ◽  
pp. 6-9
Author(s):  
Elizabeth B. Sawyer ◽  
Sarah Perrett
Keyword(s):  
Protein Misfolding ◽  
Amyloid Fibrils ◽  
Prion Diseases ◽  
Three Dimensional ◽  
Epigenetic Inheritance ◽  
Dimensional Structure ◽  
Spongiform Encephalopathy ◽  
Wide Range ◽  
The Many ◽  
And Function

The ability of proteins to recognize, bind and manipulate a wide range of other molecules lies at the heart of virtually every cellular process. In order to achieve this, proteins must fold into a precise three-dimensional structure. A failure to achieve this structure, and the associated loss of protein stability and function, results in diseases such as muscular dystrophy and cystic fibrosis. In addition, the misfolding and aggregation of proteins to form fibrillar species is associated with the progression of amyloid diseases such as Alzheimer's and Huntington's and prion diseases including Creutzfeldt– Jakob disease and bovine spongiform encephalopathy (BSE, or ‘mad cow disease’). In this article, we consider advances in the study of protein folding and misfolding and their relevance to biological function. We also explore the issue of protein ‘misfolding’ to form functional aggregated structures, such as the mode of epigenetic inheritance mediated by fungal prions and the formation of amyloid fibrils with positive biological functions in bacteria.

scholarly journals Histidine-Rich Defensins from the Solanaceae and Brasicaceae Are Antifungal and Metal Binding Proteins

2020 ◽  
Vol 6 (3) ◽  
pp. 145
Author(s):  
Mark R. Bleackley ◽  
Shaily Vasa ◽  
Peta J. Harvey ◽  
Thomas M. A. Shafee ◽  
Bomai K. Kerenga ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Metal Binding ◽  
Disulfide Bonds ◽  
Three Dimensional ◽  
Binding Activity ◽  
Dimensional Structure ◽  
Histidine Residues ◽  
Plant Defensins ◽  
Arginine Residues ◽  
Solanaceous Plants

Plant defensins are best known for their antifungal activity and contribution to the plant immune system. The defining feature of plant defensins is their three-dimensional structure known as the cysteine stabilized alpha-beta motif. This protein fold is remarkably tolerant to sequence variation with only the eight cysteines that contribute to the stabilizing disulfide bonds absolutely conserved across the family. Mature defensins are typically 46–50 amino acids in length and are enriched in lysine and/or arginine residues. Examination of a database of approximately 1200 defensin sequences revealed a subset of defensin sequences that were extended in length and were enriched in histidine residues leading to their classification as histidine-rich defensins (HRDs). Using these initial HRD sequences as a query, a search of the available sequence databases identified over 750 HRDs in solanaceous plants and 20 in brassicas. Histidine residues are known to contribute to metal binding functions in proteins leading to the hypothesis that HRDs would have metal binding properties. A selection of the HRD sequences were recombinantly expressed and purified and their antifungal and metal binding activity was characterized. Of the four HRDs that were successfully expressed all displayed some level of metal binding and two of four had antifungal activity. Structural characterization of the other HRDs identified a novel pattern of disulfide linkages in one of the HRDs that is predicted to also occur in HRDs with similar cysteine spacing. Metal binding by HRDs represents a specialization of the plant defensin fold outside of antifungal activity.

scholarly journals The Milky Way, the Galactic Halo, and the Halos of Galaxies

2015 ◽  
Vol 11 (S317) ◽  
pp. 266-271
Author(s):  
Ortwin Gerhard
Keyword(s):  
Milky Way ◽  
Galactic Halo ◽  
Large Fraction ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Galaxy Halos ◽  
The Subject ◽  
Hierarchical Nature ◽  
Tidal Streams ◽  
The Many

AbstractThe Milky Way, “our” Galaxy, is currently the subject of intense study with many ground-based surveys, in anticipation of upcoming results from the Gaia mission. From this work we have been learning about the full three-dimensional structure of the Galactic box/peanut bulge, the distribution of stars in the bar and disk, and the many streams and substructures in the Galactic halo. The data indicate that a large fraction of the Galactic halo has been accreted from outside. Similarly, in many external galaxy halos there is now evidence for tidal streams and accretion of satellites. To study these features requires exquisite, deep photometry and spectroscopy. These observations illustrate how galaxy halos are still growing, and sometimes can be used to “time” the accretion events. In comparison with cosmological simulations, the structure of galaxy halos gives us a vivid illustration of the hierarchical nature of our Universe.

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