5WZR

Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors

Sato, M.Liebschner, D.Yamada, Y.Matsugaki, N.Arakawa, T.Wills, S.S.Hattie, M.Stubbs, K.A.Ito, T.Senda, T.Ashida, H.Fushinobu, S.

(2017) J. Biol. Chem. 292: 12126-12138

  • DOI: 10.1074/jbc.M117.777391
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The α-N-acetylgalactosaminidase from the probiotic bacterium Bifidobacterium bifidum (NagBb) belongs to the glycoside hydrolase family 129 and hydrolyzes the glycosidic bond of Tn-antigen (GalNAcα1-Ser/Thr). NagBb is involved in assimilation of O-gly ...

    The α-N-acetylgalactosaminidase from the probiotic bacterium Bifidobacterium bifidum (NagBb) belongs to the glycoside hydrolase family 129 and hydrolyzes the glycosidic bond of Tn-antigen (GalNAcα1-Ser/Thr). NagBb is involved in assimilation of O-glycans on mucin glycoproteins by B. bifidum in the human gastrointestinal tract, but its catalytic mechanism has remained elusive because of a lack of sequence homology around putative catalytic residues and of other structural information. Here we report the X-ray crystal structure of NagBb, representing the first GH129 family structure, solved by the single-wavelength anomalous dispersion method based on sulfur atoms of the native protein. We determined ligand-free, GalNAc, and inhibitor complex forms of NagBb and found that Asp-435 and Glu-478 are located in the catalytic domain at appropriate positions for direct nucleophilic attack at the anomeric carbon and proton donation for the glycosidic bond oxygen, respectively. A highly conserved Asp-330 forms a hydrogen bond with the O4 hydroxyl of GalNAc in the -1 subsite, and Trp-398 provides a stacking platform for the GalNAc pyranose ring. Interestingly, a metal ion, presumably Ca2+, is involved in the recognition of the GalNAc N-acetyl group. Mutations at Asp-435, Glu-478, Asp-330, and Trp-398 and residues involved in metal coordination (including an all-Ala quadruple mutant) significantly reduced the activity, indicating that these residues and the metal ion play important roles in substrate recognition and catalysis. Interestingly, NagBb exhibited some structural similarities to the GH101 endo-α-N-acetylgalactosaminidases, but several critical differences in substrate recognition and reaction mechanism account for the different activities of these two enzymes.


    Related Citations: 
    • alpha-N-acetylgalactosaminidase from infant-associated bifidobacteria belonging to novel glycoside hydrolase family 129 is implicated in alternative mucin degradation pathway
      Kiyohara, M.,Nakatomi, T.,Kurihara, S.,Fushinobu, S.,Suzuki, H.,Tanaka, T.,Shoda, S.,Kitaoka, M.,Katayama, T.,Yamamoto, K.,Ashida, H.
      (2012) J. Biol. Chem. 287: 693


    Organizational Affiliation

    From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-N-acetylgalactosaminidase
A, B
640Bifidobacterium bifidumMutation(s): 0 
Gene Names: nagBb
EC: 3.2.1.-
Find proteins for G5ELM1 (Bifidobacterium bifidum)
Go to UniProtKB:  G5ELM1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DJN
Query on DJN

Download SDF File 
Download CCD File 
A, B
N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide
2-acetamido-1,2-dideoxy-D-galacto-nojirimycin, DGJNAc
C8 H16 N2 O4
GBRAQQUMMCVTAV-OSMVPFSASA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.628α = 90.00
b = 128.478β = 90.00
c = 176.885γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15H02443
Japan Society for the Promotion of ScienceJapan16J03683

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references