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  • 1
    ISSN: 1433-4909
    Keywords: Key words Xylanases ; Genomic walking PCR ; Multidomain enzymes ; Cellulose-binding domains ; Linker sequences ; Horizontal gene transfer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Three family 10 xylanase genes (xynA, xynB, and xynC) and a single family 11 xylanase gene (xynD) were identified from the extreme thermophile Caldicellulosiruptor strain Rt69B.1 through the use of consensus PCR in conjunction with sequencing and polyacrylamide gel electrophoresis. These genes appear to comprise the complete endoxylanase system of Rt69B.1. The xynA gene was found to be homologous to the xynA gene of the closely related Caldicellulosiruptor strain Rt8B.4, and primers designed previously to amplify the Rt8B.4 xynA gene could amplify homologous full-length xynA gene fragments from Rt69B.1. The complete nucleotide sequences of the Rt69B.1 xynB, xynC, and xynD genes were obtained using genomic walking PCR. The full-length xynB and xynC genes are more than 5 kb in length and encode highly modular enzymes that are the largest xylanases reported to date. XynB has an architecture similar to the family 10 xylanases from Thermoanaerobacterium saccharolyticum (XynA) and Clostridium thermocellum (XynX) and may be cell wall associated, while XynC is a bifunctional enzyme with an architecture similar to the bifunctional β-glycanases from Caldicellulosiruptor saccharolyticus. The xynD gene encodes a two-domain family 11 xylanase that is identical in architecture to the XynB family 11 xylanase from the unrelated extreme thermophile Dictyoglomus thermophilum strain Rt46B.1. The sequence similarities between the Rt69B.1 xylanases with respect to their evolution are discussed.
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  • 2
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Microorganisms employ a large array of enzymes to break down the cellulose and hemicelluloses of plant biomass. These enzymes, especially those with high thermal stability, have many uses in biotechnology. We have solved the crystal structure of a β-1,4-xylanase, XynB, from the extremely thermophilic bacterium Dictyoglomus thermophilum, isolate Rt46B.1. The protein crystallized from 1.6 M ammonium sulfate, 0.2 M HEPES pH 7.2 and 10% glycerol, with unit-cell parameters a = b = 91.3, c = 44.9 Å and space group P43. The structure was solved at high resolution (1.8 Å) by X-ray crystallography, using the method of isomorphous replacement with a single mercury derivative, and refined to a final R factor of 18.3% (Rfree = 22.1%). XynB has the single-domain fold typical of family 11 xylanases, comprising a jelly roll of two highly twisted β-sheets that create a deep substrate-binding cleft. The two catalytic residues, Glu90 and Glu180, occupy this cleft. Compared with other family 11 xylanases, XynB has a greater proportion of polar surface and has a slightly extended C-terminus that, combined with the extension of β-strand A5, gives additional hydrogen bonding and hydrophobic packing. These factors may account for the enhanced thermal stability of the enzyme.
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  • 3
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Many thermophilic bacteria belong to groups with deep phylogenetic lineages and ancestral forms were established before the occurrence of eucaryotes that produced cellulose and hemicellulose. Thus they may have acquired their β-glycanase genes from more recent mesophilic bacteria. Most research has focussed on extremely thermophilic eubacteria growing above 65°C under anaerobic conditions. Only recently have aerobic cellulolytic thermophiles been described from widely separated lineages (for example, Rhodothermus marinus, Caldibacillus cellulovorans). Many thermophilic bacteria produce cellulases and xylanases that have novel structures, with additional protein domains not identified with their catalytic activity. Many of these enzymes are multifunctional and code for more than one catalytic activity. This type of enzyme structure was first identified in the extreme thermophile Caldicellulosiruptor saccharolyticus. There is a general relatedness evident between catalytic domains, cellulose binding domains and other ancillary domains, which suggests that there may have been significant lateral gene transfer in the evolution of these microorganisms. Detailed molecular studies show that there is variation in the sequences of these related but not identical genes from taxonomically widely-separated organisms.
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  • 4
    Publication Date: 2000-11-01
    Print ISSN: 0907-4449
    Electronic ISSN: 1399-0047
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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