7ZZK | pdb_00007zzk

Structure of the N-acetyl-D-glucosamine oxidase from Ralstonia Solanacearum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural Elucidation and Engineering of a Bacterial Carbohydrate Oxidase.

Boverio, A.Widodo, W.S.Santema, L.L.Rozeboom, H.J.Xiang, R.Guallar, V.Mattevi, A.Fraaije, M.W.

(2023) Biochemistry 62: 429-436

  • DOI: https://doi.org/10.1021/acs.biochem.2c00307
  • Primary Citation Related Structures: 
    7ZZK

  • PubMed Abstract: 

    Flavin-dependent carbohydrate oxidases are valuable tools in biotechnological applications due to their high selectivity in the oxidation of carbohydrates. In this study, we report the biochemical and structural characterization of a recently discovered carbohydrate oxidase from the bacterium Ralstonia solanacearum , which is a member of the vanillyl alcohol oxidase flavoprotein family. Due to its exceptionally high activity toward N -acetyl-d-galactosamine and N -acetyl-d-glucosamine, the enzyme was named N -acetyl-glucosamine oxidase (NagOx). In contrast to most known (fungal) carbohydrate oxidases, NagOx could be overexpressed in a bacterial host, which facilitated detailed biochemical and enzyme engineering studies. Steady state kinetic analyses revealed that non-acetylated hexoses were also accepted as substrates albeit with lower efficiency. Upon determination of the crystal structure, structural insights into NagOx were obtained. A large cavity containing a bicovalently bound FAD, tethered via histidyl and cysteinyl linkages, was observed. Substrate docking highlighted how a single residue (Leu251) plays a key role in the accommodation of N-acetylated sugars in the active site. Upon replacement of Leu251 (L251R mutant), an enzyme variant was generated with a drastically modified substrate acceptance profile, tuned toward non-N-acetylated monosaccharides and disaccharides. Furthermore, the activity toward bulkier substrates such as the trisaccharide maltotriose was introduced by this mutation. Due to its advantage of being overexpressed in a bacterial host, NagOx can be considered a promising alternative engineerable biocatalyst for selective oxidation of monosaccharides and oligosaccharides.


  • Organizational Affiliation
    • Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 116.02 kDa 
  • Atom Count: 9,058 
  • Modeled Residue Count: 975 
  • Deposited Residue Count: 1,022 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-acetyl-D-hexosamine oxidase
A, B
511Ralstonia solanacearumMutation(s): 0 
Gene Names: RRSL_02030
EC: 1.1.3.29
UniProt
Find proteins for A3RXB7 (Ralstonia solanacearum (strain UW551))
Explore A3RXB7 
Go to UniProtKB:  A3RXB7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3RXB7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
D [auth A],
M [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A],
K [auth A],
L [auth B],
O [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth A]
I [auth A]
J [auth A]
E [auth A],
F [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA

Query on ALA



Download:Ideal Coordinates CCD File
C [auth A]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.958α = 90
b = 105.009β = 90
c = 120.671γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2023-01-25
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary