2G8S | pdb_00002g8s

Crystal structure of the soluble Aldose sugar dehydrogenase (Asd) from Escherichia coli in the apo-form

• PDB DOI: https://doi.org/10.2210/pdb2G8S/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-03 Released: 2006-08-08 
• Deposition Author(s): Southall, S.M., Doel, J.J., Richardson, D.J., Oubrie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.183 (Depositor) 
• R-Value Work: 
  0.149 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Literature

Soluble Aldose Sugar Dehydrogenase from Escherichia coli: A HIGHLY EXPOSED ACTIVE SITE CONFERRING BROAD SUBSTRATE SPECIFICITY.

Southall, S.M., Doel, J.J., Richardson, D.J., Oubrie, A.

(2006) J Biological Chem 281: 30650-30659

• PubMed: 16864586 
• DOI: https://doi.org/10.1074/jbc.M601783200
• Primary Citation Related Structures: 
  2G8S


• PubMed Abstract: 
  

  A water-soluble aldose sugar dehydrogenase (Asd) has been purified for the first time from Escherichia coli. The enzyme is able to act upon a broad range of aldose sugars, encompassing hexoses, pentoses, disaccharides, and trisaccharides, and is able to oxidize glucose to gluconolactone with subsequent hydrolysis to gluconic acid. The enzyme shows the ability to bind pyrroloquinoline quinone (PQQ) in the presence of Ca2+ in a manner that is proportional to its catalytic activity. The x-ray structure has been determined in the apo-form and as the PQQ-bound active holoenzyme. The beta-propeller fold of this protein is conserved between E. coli Asd and Acinetobacter calcoaceticus soluble glucose dehydrogenase (sGdh), with major structural differences lying in loop and surface-exposed regions. Many of the residues involved in binding the cofactor are conserved between the two enzymes, but significant differences exist in residues likely to contact substrates. PQQ is bound in a large cleft in the protein surface and is uniquely solvent-accessible compared with other PQQ enzymes. The exposed and charged nature of the active site and the activity profile of this enzyme indicate possible factors that underlie a low affinity for glucose but generic broad substrate specificity for aldose sugars. These structural and catalytic properties of the enzymes have led us to propose that E. coli Asd provides a prototype structure for a new subgroup of PQQ-dependent soluble dehydrogenases that is distinct from the A. calcoaceticus sGdh subgroup.

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Organizational Affiliation: 
• Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.23 kDa 
• Atom Count: 7,102 
• Modeled Residue Count: 695 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose/sorbosone dehydrogenases	A, B	353	Escherichia coli K-12	Mutation(s): 6  Gene Names: yliI EC: 1.1.5
UniProt
Find proteins for P75804 (Escherichia coli (strain K12)) Explore P75804  Go to UniProtKB:  P75804

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.183 (Depositor) 
• R-Value Work:  0.149 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.829	α = 90
b = 113.475	β = 90.03
c = 75.372	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Southall, S.M., Doel, J.J., Richardson, D.J., Oubrie, A.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary