5G56

THE TETRA-MODULAR CELLULOSOMAL ARABINOXYLANASE CtXyl5A STRUCTURE AS REVEALED BY X-RAY CRYSTALLOGRAPHY

Replaces:  5AK1

Summary for 5G56

• Entry DOI: 10.2210/pdb5g56/pdb
• Descriptor: CARBOHYDRATE BINDING FAMILY 6, CALCIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• Functional Keywords: carbohydrate binding protein, arabinoxylanase, ctxyl5a, gh5, cbm6, cbm13, fn3, clostridium thermocellum, cellulosome
• Biological source: CLOSTRIDIUM THERMOCELLUM
• Total number of polymer chains: 1
• Total formula weight: 94306.23

Authors

Bras, J.L.A.,Gilbert, H.J.,Ferreira, L.M.A.,Fontes, C.M.G.A.,Najmudin, S. (deposition date: 2016-05-21, release date: 2016-06-29, Last modification date: 2024-10-23)

Primary citation

Labourel, A.,Crouch, L.I.,Bras, J.L.,Jackson, A.,Rogowski, A.,Gray, J.,Yadav, M.P.,Henrissat, B.,Fontes, C.M.,Gilbert, H.J.,Najmudin, S.,Basle, A.,Cuskin, F.
The Mechanism by which Arabinoxylanases Can Recognise Highly Decorated Xylans.
J.Biol.Chem., 291:22149-, 2016

PubMed Abstract: The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. Xylan, a major component of the plant cell wall, consists of a backbone of β-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. A large penta-modular enzyme, CtXyl5A, was shown previously to specifically target arabinoxylans. The mechanism of substrate recognition displayed by the enzyme, however, remains unclear. Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. The data showed that four of the protein modules adopt a rigid structure, which stabilizes the catalytic domain. The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure, suggesting positional flexibility. The structure of the enzyme in complex with Xylp-β-1,4-Xylp-β-1,4-Xylp-[α-1,3-Araf]-β-1,4-Xylp showed that the Araf decoration linked O to the xylose in the active site is located in the pocket (-2* subsite) that abuts onto the catalytic center. The -2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. Alanine substitution of Glu, Tyr, or Asn, which interact with arabinose and xylose side chains at the -2* subsite, abrogates catalytic activity. Distal to the active site, the xylan backbone makes limited apolar contacts with the enzyme, and the hydroxyls are solvent-exposed. This explains why CtXyl5A is capable of hydrolyzing xylans that are extensively decorated and that are recalcitrant to classic endo-xylanase attack.

PubMed: 27531750
DOI: 10.1074/JBC.M116.743948

Experimental method

X-RAY DIFFRACTION (2.64 Å)