1GQJ

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

• PDB DOI: https://doi.org/10.2210/pdb1GQJ/pdb

• Classification: GLUCURONIDASE
• Organism(s): Cellvibrio japonicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-11-26 Released: 2002-09-26 
• Deposition Author(s): Nurizzo, D., Nagy, T., Gilbert, H.J., Davies, G.J.

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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 

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

• PubMed: 11937059 
• DOI: https://doi.org/10.1016/s0969-2126(02)00742-6
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 162.66 kDa 
• Atom Count: 12,991 
• Modelled Residue Count: 1,416 
• Deposited Residue Count: 1,416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-D-GLUCURONIDASE	A, B	708	Cellvibrio japonicus	Mutation(s): 0  EC: 3.2.1.139
UniProt
Find proteins for B3PC73 (Cellvibrio japonicus (strain Ueda107)) Explore B3PC73  Go to UniProtKB:  B3PC73

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	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
CO	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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	C, D	4beta-beta-xylobiose	Oligosaccharide / Metabolism

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 = 69.561	α = 115.23
b = 74.609	β = 93.15
c = 87.45	γ = 109.17

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-26 
Deposition Author(s): Nurizzo, D., Nagy, T., Gilbert, H.J., Davies, G.J.

Revision History  

• 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