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Literature summary extracted from

  • Freire, F.; Verma, A.; Bule, P.; Alves, V.; Fontes, C.; Goyal, A.; Najmudin, S.
    Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum (2016), Acta Crystallogr. Sect. D, 72, 1162-1173.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.2.1.8 structure of a truncated derivative of comprising exclusively the enzyme catalytic module. The enzyme displays a (beta/alpha)8 TIM-barrel core with a side-associated beta-sheet domain. In mutant E225A, solved in the presence of xylotetraose, xylotetraose-cleavage oligosaccharides partially occupy subsites -3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. The xylopyranosyl ring at the -1 subsite appears in the alpha-anomeric configuration Acetivibrio thermocellus
3.2.1.136 modeling of structure. The protein displays a jelly roll beta-sandwich fold presenting two potential carbohydrate binding clefts, A and B. The cleft A, is located between two loops connecting b4-b5 and b8-b9 strands. Tyr28 and Phe84 present on these loops make a planar hydrophobic binding surface to accommodate sugar ring of ligand. The cleft B, is located on concave surface of beta-sandwich fold. Tyr34 and Tyr104 make a planar hydrophobic platform, which may be inaccessible to ligand due to hindrance by Pro68 Acetivibrio thermocellus

Protein Variants

EC Number Protein Variants Comment Organism
3.2.1.8 E225A mutation in catalytic residue, crystallization data Acetivibrio thermocellus
3.2.1.136 F84A mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans Acetivibrio thermocellus
3.2.1.136 Y28A mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans Acetivibrio thermocellus
3.2.1.136 Y28A/F28A mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans Acetivibrio thermocellus

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
3.2.1.8 cellulosome
-
 Acetivibrio thermocellus 43263
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.2.1.136 Ca2+ 5 mM, slightly shifts melting temperature, does not affect structure stability and binding affinity significantly Acetivibrio thermocellus

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.2.1.8 45000
-
-
 Acetivibrio thermocellus
3.2.1.136 13800
-
-
 Acetivibrio thermocellus
3.2.1.136 14000
-
-
 Acetivibrio thermocellus

Organism

EC Number Organism UniProt Comment Textmining
3.2.1.8 Acetivibrio thermocellus A3DJS9
-
-
3.2.1.8 Acetivibrio thermocellus DSM 1237 A3DJS9
-
-
3.2.1.136 Acetivibrio thermocellus A3DJS9
-
-
3.2.1.136 Acetivibrio thermocellus DSM 1237 A3DJS9
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.1.8 additional information acts predominantly on polysaccharides with xylan as the main chain and substituted with varying amounts of glucuronic acids, such as in beechwood xylan, birchwood xylan and 4-O-methylglucuronoxylan Acetivibrio thermocellus ?
-
 ?
3.2.1.8 additional information acts predominantly on polysaccharides with xylan as the main chain and substituted with varying amounts of glucuronic acids, such as in beechwood xylan, birchwood xylan and 4-O-methylglucuronoxylan Acetivibrio thermocellus DSM 1237 ?
-
 ?
3.2.1.136 4-O-methylglucuronoxylan + H2O
-
 Acetivibrio thermocellus ?
-
 ?
3.2.1.136 beechwood xylan + H2O
-
 Acetivibrio thermocellus ?
-
 ?
3.2.1.136 beechwood xylan + H2O
-
 Acetivibrio thermocellus DSM 1237 ?
-
 ?
3.2.1.136 birchwood xylan + H2O
-
 Acetivibrio thermocellus ?
-
 ?
3.2.1.136 additional information isoform XynGH30 has high binding affinity with different xylans through an exothermic mechanism, with relatively higher affinity against arabinoxylans. The enzyme shows negligible affinity towards celluloses, pectins and other polysaccharides but predominantly interacts with ligands containing a xylan backbone (beta-1,4-xylopyranose) Acetivibrio thermocellus ?
-
 ?
3.2.1.136 additional information isoform XynGH30 has high binding affinity with different xylans through an exothermic mechanism, with relatively higher affinity against arabinoxylans. The enzyme shows negligible affinity towards celluloses, pectins and other polysaccharides but predominantly interacts with ligands containing a xylan backbone (beta-1,4-xylopyranose) Acetivibrio thermocellus DSM 1237 ?
-
 ?
3.2.1.136 oat spelt xylan + H2O
-
 Acetivibrio thermocellus ?
-
 ?
3.2.1.136 oat spelt xylan + H2O
-
 Acetivibrio thermocellus DSM 1237 ?
-
 ?
3.2.1.136 rye arabinoxylan + H2O
-
 Acetivibrio thermocellus ?
-
 ?
3.2.1.136 wheat arabinoxylan + H2O
-
 Acetivibrio thermocellus ?
-
 ?
3.2.1.136 wheat arabinoxylan + H2O
-
 Acetivibrio thermocellus DSM 1237 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.2.1.8 ? x * 45000, calcuated Acetivibrio thermocellus
3.2.1.136 ? x * 14000, SDS-PAGE, x * 13800, calculated including His-tag Acetivibrio thermocellus

Synonyms

EC Number Synonyms Comment Organism
3.2.1.8 Cthe_3012
-
 Acetivibrio thermocellus
3.2.1.8 Xyn30A
-
 Acetivibrio thermocellus
3.2.1.136 XynGH30
-
 Acetivibrio thermocellus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.2.1.8 75
-
-
 Acetivibrio thermocellus

Temperature Range [°C]

EC Number Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
3.2.1.8 40 70 more than 95% of maximum activity Acetivibrio thermocellus

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.2.1.136 82
-
 melting temperature Acetivibrio thermocellus
3.2.1.136 85
-
 melting temperature, presence of 5 mM Ca2+ Acetivibrio thermocellus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.2.1.8 6
-
-
 Acetivibrio thermocellus