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Literature summary extracted from

  • Fowler, C.A.; Hemsworth, G.R.; Cuskin, F.; Hart, S.; Turkenburg, J.; Gilbert, H.J.; Walton, P.H.; Davies, G.J.
    Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae (2018), Acta Crystallogr. Sect. D, 74, 946-955 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.2.1.8 expression in Escherichia coli BL21 with a 3C protease-removable N-terminal hexahistidine tag Teredinibacter turnerae
3.2.1.8 gene TERTU_4506, recombinant expression of codon-optimized N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3) Teredinibacter turnerae

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.2.1.8 purified wild-type enzyme TtGH8 uncomplexed and complexed with xylobiose and xylotriose, and mutant D281N complexed with xylohexaose, enzyme TtGH8 is mixed with well solution containing 0.1 M sodium acetate pH 4.6-5.2, 0.2 M NaCl, 14-24% PEG 6000, method optimization screening, X-ray diffraction structure determination and analysis at 1.4-1.8 A resolution, molecular replacement using Bacillus halodurans C-125 structure (PDB ID 1wu4) as the search model Teredinibacter turnerae
3.2.1.8 the three-dimensional structure of the enzyme is solved in uncomplexed and xylobiose-, xylotriose- and xylohexaose-bound forms at approximately 1.5 A resolution Teredinibacter turnerae

Protein Variants

EC Number Protein Variants Comment Organism
3.2.1.8 D281N site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme. The TtGH8 D281N-beta-1,4-xylohexaose complex structure reveals that, the -1 subsite sugar is in a completely ring-flipped, southern hemisphere 1C4 chair conformation. Although this allows access to a hexasaccharide complex structure, the ring-flipped -1 sugar is unlikely to be representative of a catalytically relevant conformation since its position neither allows protonation of the leaving group by Glu73 nor is there a potential reactive water. In the 1C4 chair conformation the now axial (and down) O2 occupies the position that should instead be occupied by the nucleophilic water Teredinibacter turnerae
3.2.1.8 additional information the catalytic domain is identified and truncated to remove the original signal peptide and linker region and to include an N-terminal hexahistidine tag and 3C protease cleavage site Teredinibacter turnerae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.2.1.8 marine beta-1,3-beta-1,4-xylan + H2O Teredinibacter turnerae
-
 ?
-
 ?
3.2.1.8 additional information Teredinibacter turnerae enzyme TtGH8 is effective at the degradation of xylan-based substrates, notably beta-1,4-xylan and mixed-linkage (beta-1,3/beta-1,4) marine xylan ?
-
 ?
3.2.1.8 additional information Teredinibacter turnerae ATCC 39867 enzyme TtGH8 is effective at the degradation of xylan-based substrates, notably beta-1,4-xylan and mixed-linkage (beta-1,3/beta-1,4) marine xylan ?
-
 ?
3.2.1.8 additional information Teredinibacter turnerae T7901 enzyme TtGH8 is effective at the degradation of xylan-based substrates, notably beta-1,4-xylan and mixed-linkage (beta-1,3/beta-1,4) marine xylan ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.2.1.8 Teredinibacter turnerae C5BJ89
-
-
3.2.1.8 Teredinibacter turnerae ATCC 39867 C5BJ89
-
-
3.2.1.8 Teredinibacter turnerae T7901 C5BJ89
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.2.1.8
-
 Teredinibacter turnerae
3.2.1.8 recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, tag cleavage by 3C protease, another step of nickel affinity chromatography, and gel filtration Teredinibacter turnerae

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.1.8 arabinoxylan + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 arabinoxylan + H2O
-
 Teredinibacter turnerae ATCC 39867 ?
-
 ?
3.2.1.8 arabinoxylan + H2O
-
 Teredinibacter turnerae T7901 ?
-
 ?
3.2.1.8 beta-1,4-xylan + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 beta-1,4-xylan + H2O
-
 Teredinibacter turnerae ATCC 39867 ?
-
 ?
3.2.1.8 beta-1,4-xylan + H2O
-
 Teredinibacter turnerae T7901 ?
-
 ?
3.2.1.8 beta-1,4-xylohexaose + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 beta-1,4-xylopentaose + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 beta-1,4-xylotetraose + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 birchwood xylan + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 marine beta-1,3-beta-1,4-xylan + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 mixed-linkage (beta-1,3,beta-1,4) xylan + H2O maximal activity against mixed-linkage polymeric xylans Teredinibacter turnerae ?
-
 ?
3.2.1.8 additional information enzyme TtGH8 is effective at the degradation of xylan-based substrates, notably beta-1,4-xylan and mixed-linkage (beta-1,3/beta-1,4) marine xylan Teredinibacter turnerae ?
-
 ?
3.2.1.8 additional information the enzyme TtGH8 is a xylan-active endoxylanase with six catalytically relevant subsites and notably a maximal activity towards mixed-linkage (beta-1,3/beta-1,4) marine xylan, TtGH8 catalyses the hydrolysis of beta-1,4-xylohexaose and displays maximal activity against mixed-linked marine polymeric xylans Teredinibacter turnerae ?
-
 ?
3.2.1.8 additional information enzyme TtGH8 is effective at the degradation of xylan-based substrates, notably beta-1,4-xylan and mixed-linkage (beta-1,3/beta-1,4) marine xylan Teredinibacter turnerae ATCC 39867 ?
-
 ?
3.2.1.8 additional information the enzyme TtGH8 is a xylan-active endoxylanase with six catalytically relevant subsites and notably a maximal activity towards mixed-linkage (beta-1,3/beta-1,4) marine xylan, TtGH8 catalyses the hydrolysis of beta-1,4-xylohexaose and displays maximal activity against mixed-linked marine polymeric xylans Teredinibacter turnerae ATCC 39867 ?
-
 ?
3.2.1.8 additional information enzyme TtGH8 is effective at the degradation of xylan-based substrates, notably beta-1,4-xylan and mixed-linkage (beta-1,3/beta-1,4) marine xylan Teredinibacter turnerae T7901 ?
-
 ?
3.2.1.8 additional information the enzyme TtGH8 is a xylan-active endoxylanase with six catalytically relevant subsites and notably a maximal activity towards mixed-linkage (beta-1,3/beta-1,4) marine xylan, TtGH8 catalyses the hydrolysis of beta-1,4-xylohexaose and displays maximal activity against mixed-linked marine polymeric xylans Teredinibacter turnerae T7901 ?
-
 ?
3.2.1.8 wheat arabinoxylan + H2O
-
 Teredinibacter turnerae ?
-
 ?
3.2.1.8 wheat arabinoxylan + H2O
-
 Teredinibacter turnerae ATCC 39867 ?
-
 ?
3.2.1.8 wheat arabinoxylan + H2O
-
 Teredinibacter turnerae T7901 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.2.1.8 More enzyme three-dimensional structure analysis Teredinibacter turnerae

Synonyms

EC Number Synonyms Comment Organism
3.2.1.8 endoxylanase
-
 Teredinibacter turnerae
3.2.1.8 glycoside hydrolase family 8 domain protein UniProt Teredinibacter turnerae
3.2.1.8 TERTU_4506
-
 Teredinibacter turnerae
3.2.1.8 TtGH8
-
 Teredinibacter turnerae

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.2.1.8 37
-
 assay at Teredinibacter turnerae

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.2.1.8 55.2
-
 melting temperature of apoenzyme Teredinibacter turnerae
3.2.1.8 57.3
-
 apoenzyme with xylan Teredinibacter turnerae
3.2.1.8 60.1
-
 apoenzyme with xylohexaose Teredinibacter turnerae
3.2.1.8 90
-
 purified recombinant enzyme, 20 min, inactivation Teredinibacter turnerae

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.2.1.8 6
-
 assay at Teredinibacter turnerae

General Information

EC Number General Information Comment Organism
3.2.1.8 evolution the enzyme belongs to the glycoside hydrolase family 8, GH8 Teredinibacter turnerae
3.2.1.8 additional information the enzyme has six catalytically relevant subsites, structural analysis of substrate-binding sites and the distortions of xylose within the catalytic centre, overview. Enzymatic glycoside hydrolysis involves the distortion of the reactive, -1 subsite, sugar into a variety of skew-boat and boat conformations, reflecting the requirements of inline attack and the stereoelectronic requirements of an oxocarbenium-ion-like transition state Teredinibacter turnerae
3.2.1.8 physiological function primary role in the degradation of marine polysaccharides Teredinibacter turnerae
3.2.1.8 physiological function the enzyme plays a primary role in the degradation of marine polysaccharides, potential of Teredinibacter turnerae for effective and diverse biomass degradation Teredinibacter turnerae

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.2.1.8 0.3
-
 marine beta-1,3-beta-1,4-xylan pH 6.0, 37°C, recombinant enzyme mutant D281N Teredinibacter turnerae
3.2.1.8 10.17
-
 beta-1,4-xylotetraose pH 6.0, 37°C, recombinant wild-type enzyme Teredinibacter turnerae
3.2.1.8 10.2
-
 beta-1,4-xylotetraose 37°C, pH 6.0 Teredinibacter turnerae
3.2.1.8 105
-
 arabinoxylan pH 6.0, 37°C, recombinant wild-type enzyme Teredinibacter turnerae
3.2.1.8 105
-
 wheat arabinoxylan 37°C, pH 6.0 Teredinibacter turnerae
3.2.1.8 233
-
 beta-1,4-xylopentaose 37°C, pH 6.0 Teredinibacter turnerae
3.2.1.8 233.33
-
 beta-1,4-xylopentaose pH 6.0, 37°C, recombinant wild-type enzyme Teredinibacter turnerae
3.2.1.8 300
-
 birchwood xylan pH 6.0, 37°C, recombinant wild-type enzyme Teredinibacter turnerae
3.2.1.8 300
-
 birchwood xylan 37°C, pH 6.0 Teredinibacter turnerae
3.2.1.8 1250
-
 beta-1,4-xylohexaose 37°C, pH 6.0 Teredinibacter turnerae
3.2.1.8 1259.26
-
 beta-1,4-xylohexaose pH 6.0, 37°C, recombinant wild-type enzyme Teredinibacter turnerae
3.2.1.8 2666.67
-
 marine beta-1,3-beta-1,4-xylan pH 6.0, 37°C, recombinant wild-type enzyme Teredinibacter turnerae
3.2.1.8 2666.7
-
 mixed-linkage (beta-1,3,beta-1,4) xylan 37°C, pH 6.0 Teredinibacter turnerae