1GQI

Structure of Pseudomonas cellulosa alpha-D-glucuronidase

PDB DOI: https://doi.org/10.2210/pdb1GQI/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.168 (Depositor), 0.180 (DCC)
R-Value Work:
0.133 (Depositor), 0.160 (DCC)
R-Value Observed:
0.133 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 11937059 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 162.14 kDa
Atom Count: 13,339
Modelled Residue Count: 1,416
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3PC73
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain L [auth A] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain V [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] T [auth B] I [auth A], J [auth A], K [auth A], L [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain X [auth B] MOL2 format, chain M [auth A] MOL2 format, chain X [auth B] mmCIF format, chain M [auth A] mmCIF format, chain X [auth B]	M [auth A], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain X [auth B] Interactions & Density Focus chain M [auth A] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.168 (Depositor), 0.180 (DCC)
R-Value Work: 0.133 (Depositor), 0.160 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.912	α = 115.18
b = 74.682	β = 93.14
c = 87.587	γ = 109.33

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-09-26

Deposition Author(s):

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: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

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Deposit Data

Help and Resources

1GQI

Structure of Pseudomonas cellulosa alpha-D-glucuronidase

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)