5OAR

Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Literature

Crystal structure of native beta-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide.

Skerlova, J.Blaha, J.Pachl, P.Hofbauerova, K.Kukacka, Z.Man, P.Pompach, P.Novak, P.Otwinowski, Z.Brynda, J.Vanek, O.Rezacova, P.

(2018) FEBS J 285: 580-598

  • DOI: https://doi.org/10.1111/febs.14360
  • Primary Citation of Related Structures:  
    5OAR

  • PubMed Abstract: 

    β-N-acetylhexosaminidase from the fungus Aspergillus oryzae is a secreted extracellular enzyme that cleaves chitobiose into constituent monosaccharides. It belongs to the GH 20 glycoside hydrolase family and consists of two N-glycosylated catalytic cores noncovalently associated with two 10-kDa O-glycosylated propeptides. We used X-ray diffraction and mass spectrometry to determine the structure of A. oryzae β-N-acetylhexosaminidase isolated from its natural source. The three-dimensional structure determined and refined to a resolution of 2.3 Å revealed that this enzyme is active as a uniquely tight dimeric assembly further stabilized by N- and O-glycosylation. The propeptide from one subunit forms extensive noncovalent interactions with the catalytic core of the second subunit in the dimer, and this chain swap suggests the distinctive structural mechanism of the enzyme's activation. Unique structural features of β-N-acetylhexosaminidase from A. oryzae define a very stable and robust framework suitable for biotechnological applications. The crystal structure reported here provides structural insights into the enzyme architecture as well as the detailed configuration of the active site. These insights can be applied to rational enzyme engineering.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hexosaminidase
A, C
78Aspergillus oryzaeMutation(s): 0 
EC: 3.2.1.52
UniProt
Find proteins for Q8J2T0 (Aspergillus oryzae)
Explore Q8J2T0 
Go to UniProtKB:  Q8J2T0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8J2T0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hexosaminidase
B, D
499Aspergillus oryzaeMutation(s): 0 
EC: 3.2.1.52
UniProt
Find proteins for Q8J2T0 (Aspergillus oryzae)
Explore Q8J2T0 
Go to UniProtKB:  Q8J2T0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8J2T0
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TBR
Query on TBR

Download Ideal Coordinates CCD File 
X [auth D]HEXATANTALUM DODECABROMIDE
Br12 Ta6
YWYIQTPPCOBSGN-UHFFFAOYSA-M
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth B],
W [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NGT
Query on NGT

Download Ideal Coordinates CCD File 
L [auth B],
Y [auth D]
3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
T [auth C]
U [auth C]
H [auth A],
I [auth A],
J [auth A],
T [auth C],
U [auth C],
V [auth C]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
M [auth B]
N [auth B]
AA [auth D],
BA [auth D],
CA [auth D],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.752α = 90
b = 105.752β = 90
c = 285.807γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech Republicprogram NPU I, project LO1304
Ministry of Education, Youth and Sports of the Czech RepublicCzech Republicprojects LG14009 and LM2015043 CIISB for CMS BIOCEV
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLTC17065
Czech Academy of SciencesCzech RepublicRVO 68378050
Czech Academy of SciencesCzech RepublicRVO 61388963
BIOCEVCzech RepublicERDF CZ.1.05/1.1.00/02.0109 and CZ.02.1.01/0.0/0.0/16_013/0001776
Charles University in PragueCzech RepublicUNCE 204025/2012
Charles University in PragueCzech RepublicSVV 260079/2014
Grant Agency of the Czech RepublicCzech RepublicGA15-05677S

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary