3GH5

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2009.06.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the molecular cloning and characterization of two novel beta-N-acetylhexosaminidases (beta-HEX, EC 3.2.1.52) from Paenibacillus sp. strain TS12. The two beta-HEXs (Hex1 and Hex2) were 70% identical in primary structure, and the N-terminal r ...

    We report the molecular cloning and characterization of two novel beta-N-acetylhexosaminidases (beta-HEX, EC 3.2.1.52) 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
beta-hexosaminidase
A
525Paenibacillus spMutation(s): 0 
Gene Names: Hex1
Find proteins for D0VX21 (Paenibacillus sp)
Go to UniProtKB:  D0VX21
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.149 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 95.328α = 90.00
b = 101.734β = 90.00
c = 107.818γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2014-02-12
    Type: Database references