1GQK | pdb_00001gqk

Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.186 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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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: https://doi.org/10.1016/s0969-2126(02)00742-6
  • Primary Citation Related Structures: 
    1GQI, 1GQJ, 1GQK, 1GQL

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 162.48 kDa 
  • Atom Count: 12,837 
  • Modeled Residue Count: 1,416 
  • Deposited Residue Count: 1,416 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALPHA-D-GLUCURONIDASE
A, B
708Cellvibrio japonicusMutation(s): 0 
EC: 3.2.1.139 (PDB Primary Data), 3.2.1 (UniProt)
UniProt
Find proteins for B3PC73 (Cellvibrio japonicus (strain Ueda107))
Explore B3PC73 
Go to UniProtKB:  B3PC73
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3PC73
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BDP

Query on BDP


Download:Ideal Coordinates CCD File
C [auth A],
N [auth B]		beta-D-glucopyranuronic acid
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [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
CO

Query on CO


Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
M [auth A]
U [auth B]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.186 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.707α = 115.34
b = 74.879β = 93.06
c = 87.481γ = 109.2
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: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary