9XDX

Chitodextrinase catalytic and C-terminal domain in complex with allosamidin from Vibrio cholerae

Summary for 9XDX

• Entry DOI: 10.2210/pdb9xdx/pdb
• Related PRD ID: PRD_000468
• Descriptor: Chitodextrinase, 2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose, ALLOSAMIZOLINE, ... (5 entities in total)
• Functional Keywords: chitodextrinase, hydrolase
• Biological source: Vibrio cholerae M66-2
• Total number of polymer chains: 1
• Total formula weight: 110080.46

Authors

Khumnonkhro, K.,Fukamizo, T.,Robinson, R.C.,Suginta, W. (deposition date: 2025-10-27, release date: 2026-08-26)

Primary citation

Khumnonkhro, K.,Chongrungreang, T.,Sakuda, S.,Robinson, R.C.,Fukamizo, T.,Suginta, W.
Structure-based functionality of a multi-domain periplasmic chitodextrinase from marine bacterium Vibrio cholerae.
J.Biol.Chem., 302:113351-113351, 2026

PubMed Abstract: Periplasmic chitodextrinase (Chdx) is involved in chitin metabolism in Vibrio species. Chdxs from Vibrio cholerae (VcChdx) and Vibrio harveyi consist of six domains: an N-terminal family 5/12 carbohydrate-binding module (N-CBM), two immunoglobulin-like domains (IgL-1 and IgL-2), a GH18 catalytic domain (CatD), a chitin-binding domain (ChBD), and a C-terminal family 5/12 carbohydrate-binding module (C-CBM). We produced recombinant VcChdx, which exhibited a single band at 116 kDa on SDS-PAGE. VcChdx fwas successfully crystallized in the ligand-free and bound state with the inhibitor allosamidin, providing insights into the catalytic center and substrate-binding groove of CatD, which tightly interacts with ChBD. However, no electron density was observed for two CBMs and two IgLs, probably due to their high conformational mobility. Size-exclusion chromatography coupled with multi-angle light scattering and small-angle X-ray scattering revealed the overall architecture of multi-modular VcChdx, in which the individual folded domains are extended in solution. Isothermal titration calorimetry analysis indicated that the interaction between VcChdx and allosamidin was enthalpy-driven with moderate affinity (K = 1.58 ± 0.48 μm). HPLC analysis of the reaction products from the substrates, chitooligosaccharides, (GlcNAc) (n = 2-6), indicated that VcChdx hydrolyzes (GlcNAc) in an endo-splitting manner. Among tested substrates, the specific activity was highest toward (GlcNAc). Taken together, VcChdx is a GH18 enzyme with an elongated, multi-modular structure and endo-splitting activity toward soluble (GlcNAc). It likely acts cooperatively with chitoporin localized to the outer membrane, which preferentially translocates (GlcNAc) into the periplasm.

PubMed: 42480705
DOI: 10.1016/j.jbc.2026.113351

Experimental method

X-RAY DIFFRACTION (3.5 Å)