Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

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Molecular cloning and crystal structural analysis of a novel beta-N-acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids

Sumida, T.Ishii, R.Yanagisawa, T.Yokoyama, S.Ito, M.

(2009) J Mol Biol 392: 87-99

  • DOI: https://doi.org/10.1016/j.jmb.2009.06.025
  • Primary Citation of Related Structures:  
    3GH4, 3GH5, 3GH7

  • PubMed Abstract: 

    We report the molecular cloning and characterization of two novel beta-N-acetylhexosaminidases (beta-HEX, EC from Paenibacillus sp. strain TS12. The two beta-HEXs (Hex1 and Hex2) were 70% identical in primary structure, and the N-terminal region of both enzymes showed significant similarity with beta-HEXs belonging to glycoside hydrolase family 20 (GH20). Interestingly, however, the C-terminal region of Hex1 and Hex2 shared no sequence similarity with the GH20 beta-HEXs or other known proteins. Both recombinant enzymes, expressed in Escherichia coli BL21(DE3), hydrolyzed the beta-N-acetylhexosamine linkage of chitooligosaccharides and glycosphingolipids such as asialo GM2 and Gb4Cer in the absence of detergent. However, the enzyme was not able to hydrolyze GM2 ganglioside in the presence or in the absence of detergent. We determined three crystal structures of Hex1; the Hex1 deletion mutant Hex1-DeltaC at a resolution of 1.8 A; Hex1-DeltaC in complex with beta-N-acetylglucosamine at 1.6 A; and Hex1-DeltaC in complex with beta-N-acetylgalactosamine at 1.9 A. We made a docking model of Hex1-DeltaC with GM2 oligosaccharide, revealing that the sialic acid residue of GM2 could hinder access of the substrate to the active site cavity. This is the first report describing the molecular cloning, characterization and X-ray structure of a procaryotic beta-HEX capable of hydrolyzing glycosphingolipids.

  • Organizational Affiliation

    Department of Bioscience and Biotechnology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-hexosaminidase525Paenibacillus sp.Mutation(s): 0 
Gene Names: Hex1
Find proteins for D0VX21 (Paenibacillus sp)
Explore D0VX21 
Go to UniProtKB:  D0VX21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VX21
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.615α = 90
b = 101.981β = 90
c = 107.622γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description