Flap endonuclease is a structure-specific nuclease which cleaves 5'-flap of bifurcated DNA substrates. Genome sequence of Thermococcus kodakarensis harbors an open reading frame, Tk1281, exhibiting high homology with archaeal flap endonucleases 1. The corresponding gene was cloned and expressed in Escherichia coli, and the gene product was purified to apparent homogeneity. Tk1281 was a monomer of 38 kDa and catalyzed the cleavage of 5'-flap from double-stranded DNA substrate containing single-stranded DNA flap. The highest cleavage activity was observed at 80 °C and pH 7.5. Under optimal conditions, Tk1281 exhibited apparent Vmax and Km values of 278 nmol/min/mg and 37 μM, respectively, against a 54-nucleotide double-stranded substrate containing a single-stranded 5'-flap of 27 nucleotides. A unique feature of Tk1281 is its highest activation in the presence of Co2+ and no activation with Mn2+. To the best of our knowledge, this is the first cloning and characterization of a flap endonuclease from the genus Thermococcus.
- MeSH
- "flap" endonukleasy chemie genetika metabolismus MeSH
- bakteriální proteiny chemie genetika metabolismus MeSH
- kinetika MeSH
- klonování DNA * MeSH
- molekulová hmotnost MeSH
- stabilita enzymů MeSH
- substrátová specifita MeSH
- Thermococcus chemie enzymologie genetika MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- "flap" endonukleasy MeSH
- bakteriální proteiny MeSH
Almost 25 years have passed since the discovery of a planktonic, heterotrophic, hyperthermophilic archaeon named Thermococcus kodakarensis KOD1, previously known as Pyrococcus sp. KOD1, by Imanaka and coworkers. T. kodakarensis is one of the most studied archaeon in terms of metabolic pathways, available genomic resources, established genetic engineering techniques, reporter constructs, in vitro transcription/translation machinery, and gene expression/gene knockout systems. In addition to all these, ease of growth using various carbon sources makes it a facile archaeal model organism. Here, in this review, an attempt is made to reflect what we have learnt from this hyperthermophilic archaeon.
- MeSH
- archeální proteiny genetika MeSH
- metabolické sítě a dráhy MeSH
- Thermococcus genetika růst a vývoj metabolismus MeSH
- vysoká teplota MeSH
- výzkum trendy MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- archeální proteiny MeSH
The haloacid dehalogenase (HAD) superfamily is one of the largest known groups of enzymes and the majority of its members catalyze the hydrolysis of phosphoric acid monoesters into a phosphate ion and an alcohol. Despite the fact that sequence similarity between HAD phosphatases is generally very low, the members of the family possess some characteristic features, such as a Rossmann-like fold, HAD signature motifs or the requirement for Mg2+ ion as an obligatory cofactor. This study focuses on a new hypothetical HAD phosphatase from Thermococcus thioreducens. The protein crystallized in space group P21212, with unit-cell parameters a = 66.3, b = 117.0, c = 33.8 Å, and the crystals contained one molecule in the asymmetric unit. The protein structure was determined by X-ray crystallography and was refined to 1.75 Å resolution. The structure revealed a putative active site common to all HAD members. Computational docking into the crystal structure was used to propose substrates of the enzyme. The activity of this thermophilic enzyme towards several of the selected substrates was confirmed at temperatures of 37°C as well as 60°C.
- Klíčová slova
- HAD superfamily, crystal structure, docking, hypothetical phosphatase, phosphatase assay,
- MeSH
- fosfatasy chemie MeSH
- hydrolasy chemie MeSH
- katalytická doména MeSH
- kinetika MeSH
- krystalografie rentgenová metody MeSH
- molekulární modely MeSH
- substrátová specifita MeSH
- Thermococcus enzymologie MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- 2-haloacid dehalogenase MeSH Prohlížeč
- fosfatasy MeSH
- hydrolasy MeSH
Enzymatic depolymerization of chitosan, a β-(1,4)-linked polycationic polysaccharide composed of d-glucosamine (GlcN) and N-acetyl-d-glucosamine (GlcNAc) provides a possible route to the exploitation of chitin-rich biomass. Complete conversion of chitosan to mono-sugars requires the synergistic action of endo- and exo- chitosanases. In the present study we have developed an efficient and cost-effective chitosan-degrading enzyme cocktail containing only two enzymes, an endo-attacking bacterial chitosanase, ScCsn46A, from Streptomyces coelicolor, and an exo-attacking glucosamine specific β-glucosaminidase, Tk-Glm, from the archaeon Thermococcus kodakarensis KOD1. Moreover, we developed a fast, reliable quantitative method for analysis of GlcN using high performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD). The sensitivity of this method is high and less than 50 pmol was easily detected, which is about 1000-fold better than the sensitivity of more commonly used detection methods based on refractive index. We also obtained qualitative insight into product development during the enzymatic degradation reaction by means of ElectroSpray Ionization-Mass Spectrometry (ESI-MS).
- Klíčová slova
- Chitosan, Chitosanase, Glucosamine, HPAEC-PAD, N-acetyl-d-glucosamine (PubChem CID:439174), d-glucosamine (PubChem CID:439213), exo-β-glucosaminidase,
- MeSH
- bakteriální proteiny metabolismus MeSH
- beta-glukosidasa metabolismus MeSH
- chitosan chemie MeSH
- chromatografie iontoměničová metody MeSH
- glukosamin analýza chemie MeSH
- glykosidhydrolasy metabolismus MeSH
- hmotnostní spektrometrie s elektrosprejovou ionizací MeSH
- Streptococcus enzymologie MeSH
- substrátová specifita MeSH
- Thermococcus enzymologie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- bakteriální proteiny MeSH
- beta-glukosidasa MeSH
- chitosan MeSH
- chitosanase MeSH Prohlížeč
- glukosamin MeSH
- glykosidhydrolasy MeSH
A simple and elegant method for inhibition of non-templated nucleotide addition by DNA polymerases and for following DNA 3'-heterogeneity in enzymatic DNA synthesis by primer extension (PEX) is described. When template bearing ortho-twisted intercalating nucleic acid (ortho-TINA) at the 5'-end is used, non-templated nucleotide addition is reduced in both the A- and B-family DNA polymerases (KOD XL, KOD (exo-), Bst 2.0, Therminator, Deep Vent (exo-) and Taq). Formation of a single oligonucleotide product was observed with ortho-TINA modified template and KOD XL, KOD (exo-), Bst 2.0, Deep Vent (exo-) and Taq DNA polymerases. This approach can be applied to the synthesis of both unmodified and base-modified oligonucleotides.
- Klíčová slova
- DNA polymerases, Nucleotide addition, Oligonucleotides, Primer extension, Twisted intercalating nucleic acid,
- MeSH
- biotin chemie MeSH
- DNA-dependentní DNA-polymerasy chemie genetika MeSH
- DNA chemie genetika MeSH
- Geobacillus stearothermophilus enzymologie MeSH
- interkalátory chemie MeSH
- pyreny chemie MeSH
- Pyrococcus MeSH
- Thermococcus enzymologie MeSH
- Thermus enzymologie MeSH
- tritylové sloučeniny chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- biotin MeSH
- DNA-dependentní DNA-polymerasy MeSH
- DNA MeSH
- interkalátory MeSH
- pyreny MeSH
- tritylové sloučeniny MeSH
We investigated the effect of temperature on the binding specificity of the recombinant d-trehalose/d-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis (TMBP). Importantly, we found that TMBP can bind d-glucose (Glc). The Glc binding was characterized by means of fluorescence spectroscopy in the temperature range of 25 degrees C-85 degrees C. Our results show that at 25 degrees C the binding of Glc to TMBP is well represented by a bimodal model with apparent K(d) of 20 muM and approximately 3-8 mM for the first and the second binding step, respectively. At 60 degrees C the binding of Glc to TMBP is represented by a simple hyperbolic model with an apparent K(d) value of about 40 muM. Finally, at 85 degrees C Glc did not bind to TMBP. Molecular dynamics (MD) simulations were used to shed light on the molecular mechanism of the Glc binding. Our results suggest that after proper fluorescent labeling TMBP can be used as a highly thermostable and non-consuming analyte biosensor for monitoring the level of glucose in fluids (e.g. human blood) where other sugars are not present.
- MeSH
- archeální proteiny metabolismus MeSH
- fluorescenční spektrometrie MeSH
- maltosa metabolismus MeSH
- molekulární modely MeSH
- teplota MeSH
- Thermococcus izolace a purifikace metabolismus MeSH
- trehalosa metabolismus MeSH
- vazba proteinů MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- archeální proteiny MeSH
- maltosa MeSH
- trehalosa MeSH
In this work, we used fluorescence spectroscopy, molecular dynamics simulation, and Fourier transform infrared spectroscopy for investigating the effect of trehalose binding and maltose binding on the structural properties and the physical parameters of the recombinant D-trehalose/D-maltose binding protein (TMBP) from the hyperthermophilic archaeon Thermococcus litoralis. The binding of the two sugars to TMBP was studied in the temperature range 20 degrees-100 degrees C. The results show that TMBP possesses remarkable temperature stability and its secondary structure does not melt up to 90 degrees C. Although both the secondary structure itself and the sequence of melting events were not significantly affected by the sugar binding, the protein assumes different conformations with different physical properties depending whether maltose or trehalose is bound to the protein. At low and moderate temperatures, TMBP possesses a structure that is highly compact both in the absence and in the presence of two sugars. At about 90 degrees C, the structure of the unliganded TMBP partially relaxes whereas both the TMBP/maltose and the TMBP/trehalose complexes remain in the compact state. In addition, Fourier transform infrared results show that the population of alpha-helices exposed to the solvent was smaller in the absence than in the presence of the two sugars. The spectroscopic results are supported by molecular dynamics simulations. Our data on dynamics and stability of TMBP can contribute to a better understanding of transport-related functions of TMBP and constitute ground for targeted modifications of this protein for potential biotechnological applications.
- MeSH
- časové faktory MeSH
- fluorescenční spektrometrie MeSH
- maltosa chemie metabolismus MeSH
- molekulární modely MeSH
- počítačová simulace MeSH
- proteiny vázající maltosu MeSH
- sbalování proteinů MeSH
- spektrofotometrie infračervená MeSH
- substrátová specifita MeSH
- teplota MeSH
- terciární struktura proteinů MeSH
- Thermococcus chemie metabolismus MeSH
- transportní proteiny chemie metabolismus MeSH
- trehalosa chemie metabolismus MeSH
- vazba proteinů MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- maltosa MeSH
- proteiny vázající maltosu MeSH
- transportní proteiny MeSH
- trehalosa MeSH
