8QK1 | pdb_00008qk1

Crystal structure of Trichuris suis beta-N-acetyl-D-hexosaminidase - HEX-2 in apo form

• PDB DOI: https://doi.org/10.2210/pdb8QK1/pdb

• Classification: HYDROLASE
• Organism(s): Trichuris suis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2023-09-14 Released: 2024-06-26 
• Deposition Author(s): Dutkiewicz, Z., Varrot, A.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.196 (DCC) 

Starting Model: in silico

Literature

Bioinformatic, Enzymatic, and Structural Characterization of Trichuris suis Hexosaminidase HEX-2.

Dutkiewicz, Z., Varrot, A., Breese, K.J., Stubbs, K.A., Nuschy, L., Adduci, I., Paschinger, K., Wilson, I.B.H.

(2024) Biochemistry 63: 1941-1954

• PubMed: 39058279 
• DOI: https://doi.org/10.1021/acs.biochem.4c00187
• Primary Citation Related Structures: 
  8QK1


• PubMed Abstract: 
  

  Hexosaminidases are key enzymes in glycoconjugate metabolism and occur in all kingdoms of life. Here, we have investigated the phylogeny of the GH20 glycosyl hydrolase family in nematodes and identified a β-hexosaminidase subclade present only in the Dorylaimia. We have expressed one of these, HEX-2 from Trichuris suis , a porcine parasite, and shown that it prefers an aryl β- N -acetylgalactosaminide in vitro . HEX-2 has an almost neutral pH optimum and is best inhibited by GalNAc-isofagomine. Toward N-glycan substrates, it displays a preference for the removal of GalNAc residues from LacdiNAc motifs as well as the GlcNAc attached to the α1,3-linked core mannose. Therefore, it has a broader specificity than insect fused lobe (FDL) hexosaminidases but one narrower than distant homologues from plants. Its X-ray crystal structure, the first of any subfamily 1 GH20 hexosaminidase to be determined, is closest to Streptococcus pneumoniae GH20C and the active site is predicted to be compatible with accommodating both GalNAc and GlcNAc. The new structure extends our knowledge about this large enzyme family, particularly as T. suis HEX-2 also possesses the key glutamate residue found in human hexosaminidases of either GH20 subfamily, including HEXD whose biological function remains elusive.

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Organizational Affiliation: 
• Institut für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria.
Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France.
School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia.
Institut für Parasitologie, Department für Pathobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Wien A-1210, Austria.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.33 kDa 
• Atom Count: 3,734 
• Modeled Residue Count: 456 
• Deposited Residue Count: 545 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-N-acetylhexosaminidase	A	545	Trichuris suis	Mutation(s): 0  Gene Names: M514_07548 EC: 3.2.1.52
UniProt
Find proteins for A0A085NCI8 (Trichuris suis) Explore A0A085NCI8  Go to UniProtKB:  A0A085NCI8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.196 (DCC) 

Diffraction Data: https://doi.org/10.5281/zenodo.8367522

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.118	α = 90
b = 59.044	β = 114.486
c = 105.977	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Dutkiewicz, Z., Varrot, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	W1224

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2026-01-14
  Changes: Database references