1H41

Pseudomonas cellulosa E292A alpha-D-glucuronidase mutant complexed with aldotriuronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.118 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Alpha-Glucuronidase,Glca67A,of Cellvibrio Japonicus Utilizes the Carboxylate and Methyl Groups of Aldobiouronic Acid as Important Substrate Recognition Determinants

Nagy, T.Nurizzo, D.Davies, G.J.Biely, P.Lakey, J.H.Bolam, D.N.Gilbert, H.J.

(2003) J Biol Chem 278: 20286

  • DOI: 10.1074/jbc.M302205200
  • Primary Citation of Related Structures:  
    1H41

  • PubMed Abstract: 
  • alpha-Glucuronidases are key components of the ensemble of enzymes that degrade the plant cell wall. They hydrolyze the alpha1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid (4-O-MeGlcA) and the xylan or xylooligosaccharide backbone. Here we report the crystal structure of an inactive mutant (E292A) of the alpha-glucuronidase, GlcA67A, from Cellvibrio japonicus in complex with its substrate ...

    alpha-Glucuronidases are key components of the ensemble of enzymes that degrade the plant cell wall. They hydrolyze the alpha1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid (4-O-MeGlcA) and the xylan or xylooligosaccharide backbone. Here we report the crystal structure of an inactive mutant (E292A) of the alpha-glucuronidase, GlcA67A, from Cellvibrio japonicus in complex with its substrate. The data show that the 4-O-methyl group of the substrate is accommodated within a hydrophobic sheath flanked by Val-210 and Trp-160, whereas the carboxylate moiety is located within a positively charged region of the substrate-binding pocket. The carboxylate side chains of Glu-393 and Asp-365, on the "beta-face" of 4-O-MeGlcA, form hydrogen bonds with a water molecule that is perfectly positioned to mount a nucleophilic attack at the anomeric carbon of the target glycosidic bond, providing further support for the view that, singly or together, these amino acids function as the catalytic base. The capacity of reaction products and product analogues to inhibit GlcA67A shows that the 4-O-methyl group, the carboxylate, and the xylose sugar of aldobiouronic acid all play an important role in substrate binding. Site-directed mutagenesis informed by the crystal structure of enzyme-ligand complexes was used to probe the importance of highly conserved residues at the active site of GlcA67A. The biochemical properties of K288A, R325A, and K360A show that a constellation of three basic amino acids (Lys-288, Arg-325, and Lys-360) plays a critical role in binding the carboxylate moiety of 4-O-MeGlcA. Disruption of the apolar nature of the pocket created by Val-210 (V210N and V210S) has a detrimental effect on substrate binding, although the reduction in affinity is not reflected by an inability to accommodate the 4-O-methyl group. Replacing the two tryptophan residues that stack against the sugar rings of the substrate with alanine (W160A and W543A) greatly reduced activity.


    Organizational Affiliation

    School of Cell and Molecular Biosciences, The University of Newcastle upon Tyne, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-GLUCURONIDASEA, B708Cellvibrio japonicusMutation(s): 1 
EC: 3.2.1.139 (PDB Primary Data), 3.2.1.131 (UniProt)
UniProt
Find proteins for B3PC73 (Cellvibrio japonicus (strain Ueda107))
Explore B3PC73 
Go to UniProtKB:  B3PC73
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCV (Subject of Investigation/LOI)
Query on GCV

Download Ideal Coordinates CCD File 
C [auth A], W [auth B]4-O-methyl-alpha-D-glucopyranuronic acid
C7 H12 O7
WGLLPAPKWFDHHV-NRGGUMNKSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , D [auth A] , DA [auth B] , E [auth A] , EA [auth B] , F [auth A] , 
AA [auth B],  BA [auth B],  CA [auth B],  D [auth A],  DA [auth B],  E [auth A],  EA [auth B],  F [auth A],  FA [auth B],  G [auth A],  GA [auth B],  H [auth A],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  JA [auth B],  K [auth A],  KA [auth B],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  X [auth B],  Y [auth B],  Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
LA [auth B] , MA [auth B] , NA [auth B] , OA [auth B] , PA [auth B] , R [auth A] , S [auth A] , T [auth A] , 
LA [auth B],  MA [auth B],  NA [auth B],  OA [auth B],  PA [auth B],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.118 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.412α = 115.09
b = 74.393β = 93.04
c = 87.462γ = 109.44
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary