1GQJ

Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with xylobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The Structural Basis for Catalysis and Specificity of the Pseudomonas Cellulosa Alpha-Glucuronidase, Glca67A

Nurizzo, D.Nagy, T.Gilbert, H.J.Davies, G.J.

(2002) Structure 10: 547

  • DOI: 10.1016/s0969-2126(02)00742-6
  • Primary Citation of Related Structures:  
    1GQL, 1GQK, 1GQJ, 1GQI

  • PubMed Abstract: 
  • Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. The structure of the alpha-glucuronidase, GlcA67A, from Pseudomonas cellulosa reveals three domains, the central of which is a (beta/alpha)(8) barrel housing the catalytic apparatus ...

    Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. The structure of the alpha-glucuronidase, GlcA67A, from Pseudomonas cellulosa reveals three domains, the central of which is a (beta/alpha)(8) barrel housing the catalytic apparatus. Complexes of the enzyme with the individual reaction products, either xylobiose or glucuronic acid, and the ternary complex of both glucuronic acid and xylotriose reveal a "blind" pocket which selects for short decorated xylooligosaccharides substituted with the uronic acid at their nonreducing end, consistent with kinetic data. The catalytic center reveals a constellation of carboxylates; Glu292 is poised to provide protonic assistance to leaving group departure with Glu393 and Asp365 both appropriately positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-D-GLUCURONIDASEA, B708Cellvibrio japonicusMutation(s): 0 
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
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranoseC, D2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G87728WL
GlyCosmos:  G87728WL
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , O [auth B] , P [auth B] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
K [auth A], L [auth A], M [auth A], N [auth A], U [auth B], V [auth B], W [auth B], X [auth B]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900116
Query on PRD_900116
C, D4beta-beta-xylobioseOligosaccharide /  Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.561α = 115.23
b = 74.609β = 93.15
c = 87.45γ = 109.17
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-26
    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: 2019-09-25
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary