1GQL

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

• PDB DOI: https://doi.org/10.2210/pdb1GQL/pdb

• Classification: HYDROLASE
• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.172 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 

Starting Model: experimental

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.

---

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 162.99 kDa 
• Atom Count: 12,936 
• Modelled Residue Count: 1,401 
• 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 (PDB Primary Data), 3.2.1.131 (UniProt)
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-(1-1)-beta-D-xylopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G23983GF GlyCosmos:  G23983GF

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDP	E [auth A], O [auth B]	beta-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-QIUUJYRFSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO	K [auth A], L [auth A], M [auth A], N [auth A], V [auth B], W [auth B], X [auth B], Y [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.172 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.256	α = 115.15
b = 74.323	β = 92.94
c = 87.273	γ = 109.24

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: 2017-07-05
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary