The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100 °C, have been determined by X‐ray crystallography to a resolution of 1.8 å. Crystals of this rubredoxin grow in space group P212121 with room temperature cell dimensions a = 34.6 å, b = 35.5 å, and c = 44.4 å. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X‐PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 å and 2.06°, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 å and in bond angles of 1.95°. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen‐bonding network in the β‐sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino‐terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.

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The three-dimensional solution-state structure is reported for the zinc-substituted form of rubredoxin (Rd) from the marine hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 " c . Structures were generated with DSPACEB by a hybrid distance geometry (DG)-based simulated annealing (SA) approach that employed 403 nuclear Overhauser effect (N0E)-derived interproton distance restraints, including 67 interresidue, 124 sequential ( i -j = I), 75 medium-range ( i -j = 2-5), and 137 long-range ( i -j > 5) restraints.All lower interproton distance bounds were set at the sum of the van Der Waals radii (1.8 A), and upper bounds of 2.7 A, 3.3 A, and 5.0 A were employed to represent qualitatively observed strong, medium, and weak NOE cross peak intensities, respectively. Twenty-three backbone-backbone, six backbone-sulfur (Cys), two backboneside chain, and two side chain-side chain hydrogen bond restraints were include for structure refinement, yielding a total of 436 nonbonded restraints, which averages to >16 restraints per residue. A total of 10 structures generated from random atom positions and 30 structures generated by molecular replacement using the backbone coordinates of Clostridiumpusteuriunum Rd converged to a common conformation, with the average penalty (= sum of the square of the distance bounds violations; +standard deviation) of 0.024 f 0.003 A 2 and a maximum total penalty of 0.035 A*. Superposition of the backbone atoms (C, Ca, N) of residues A1-L51 for all 40 structures afforded an average pairwise root mean square (rms) deviation value (fSD) of 0.42 f 0.07 A. Superposition of all heavy atoms for residues AI-L51, including those of structurally undefined external side chains, afforded an average pairwise rms deviation of 0.72 k 0.08 A . Qualitative comparison of back-calculated and experimental two-dimensional NOESY spectra indicate that the DG/SA structures are consistent with the experimental spectra. The global folding of P. furiosus Zn(Rd) is remarkably similar to the folding observed by X-ray crystallography for native Rd from the mesophilic organism C. pusteuriunum, with the average rms deviation value for backbone atoms of residues Al-LSI of P. furiosus Zn(Rd) superposed with respect to residues K2-V52 of C. pusteuriunum Rd of 0.77 +_ 0.06 A. The conformations of aromatic residues that compose the hydrophobic cores of the two proteins are also similar. However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions. Four of these interactions involve the nonconservatively substituted Glu 14, Ala 1, and Trp 3 residues. The combined findings are consistent with the proposal that stabilization of the N-terminal residues inhibits the &sheet from "unzipping" at elevated temperatures (Blake, P.R., Park, J.-B., Bryant, EO., et al., 1991, Biochemistry30, 10885-10895). In view of the high structural similarities between this hyperthermophilic protein and C...

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The objectives of this study were to analyze antioxidant activities and identify volatile compounds in mixed berry juice after fermentation by lactic acid bacteria (LAB). Antioxidant activity of the mixed berry juice increased significantly from 209.57±2.93 to 268.30±1.75 μmol TE/g after 24 h of fermentation. After LAB fermentation, 34 volatile compounds were identified. Among them, three compounds-benzoic acid, benzaldehyde, and vitispirane-showed significant changes in their concentrations. Peak areas of benzoic acid and benzaldehyde, which are known to possess antioxidant activities, increased by 64 and 188%, respectively, after fermentation. However, the peak area of vitispirane, which is the most abundant terpene compound in berry juices, decreased by 92% after fermentation.

The three-dimensional X-ray structures of the oxidized and reduced forms of rubredoxin from Pyrococcus furiosus, determined at -161 "C, and the NMR structure of the zinc-substituted protein, determined in solution at 45 "C, are compared. The NMR and X-ray structures, which were determined independently, are very similar and lead to similar conclusions regarding the interactions that confer hyperthermostability.Keywords: distance geometry; hyperthermophile; iron-sulfur protein; NMR structure; protein structure; rubredoxin; X-ray structure; zinc substitutionThe two companion papers (this issue: Blake et al., 1992;Day et al., 1992) describe X-ray and NMR structure determinations of rubredoxin (Rd) from the hyperthermophilic archaebacterium Pyrococcus furiosus. X-ray structure analyses were performed on the oxidized and reduced forms of the protein (Rd-ox and Rd-red) at -161 "C, and NMR studies were performed on the zincsubstituted form of the protein (Zn(Rd)) in solution at 45 "C. In this paper, we briefly compare the results of the X-ray and NMR structural studies. DiscussionAs indicated in Blake et al. (1992) and Day et al. (1992), the NMR and X-ray structures o f P. furiosus Rd were found to be conformationally similar to the X-ray structure of Rd from the mesophile Clostridiumpasteurianum. Thus, as expected, the X-ray structures of P. furiosus Rd-ox and Rd-red and the NMR structure of the Zn(Rd) are also similar to each other. Superposition of the back- respectively. Thus, the rms deviation of the backbone atoms for residues Al-LS 1 of the X-ray and NMR structures is just slightly greater (0.20 A ) than the rms deviations among the NMR structures alone.The only notable differences involving the backbone atoms of the NMR and X-ray structures occur at the C-terminal residues. Whereas the NMR data indicate that residues Glu 52 and Asp 53 exist in rapid dynamic equilibrium in solution (as reflected by the high deviations in the C a positions; Fig. 2), in crystals the conformations of these residues are restricted due to their involvement in lattice contacts. Even so, there is evidence for confor-1522

Background Simultaneous cofermentation of glucose and xylose mixtures would be a cost-effective solution for the conversion of cellulosic biomass to high-value products. However, most yeasts ferment glucose and xylose sequentially due to glucose catabolite repression. A well known thermotolerant yeast, Kluyveromyces marxianus , was selected for this work because it possesses cost-effective advantages over Saccharomyces cerevisiae for biofuel production from cellulosic biomass. Results In the present study, we employed a directed evolutionary approach using 2-deoxyglucose to develop a thermotolerant mutant capable of simultaneous cofermentation of glucose and xylose by alleviating catabolite repression. The selected mutant, K. marxianus SBK1, simultaneously cofermented 40 g/L glucose and 28 g/L xylose to produce 23.82 g/L ethanol at 40 °C. This outcome corresponded to a yield of 0.35 g/g and productivity of 0.33 g/L h, representing an 84% and 129% improvement, respectively, over the parental strain. Interestingly, following mutagenesis the overall transcriptome of the glycolysis pathway was highly downregulated in K. marxianus SBK1, except for glucokinase-1 (GLK1) which was 21-fold upregulated. Amino acid sequence of GLK1 from K. marxianus SBK1 revealed three amino acid mutations which led to more than 22-fold lower enzymatic activity compared to the parental strain. Conclusions We herein successfully demonstrated that the cofermentation of a sugar mixture is a promising strategy for the efficient utilization of cellulosic biomass by K. marxianus SBK1. Through introduction of additional biosynthetic pathways, K. marxianus SBK1 could become a chassis-type strain for the production of fuels and chemicals from cellulosic biomass. Electronic supplementary material The online version of this article (10.1186/s13068-019-1431-x) contains supplementary material, which is available to authorized users.