2G8S

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.183
R-Value Work: 0.149
R-Value Observed: 0.148

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Biol Chem 281: 30650-30659

PubMed: 16864586 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M601783200
Primary Citation of 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.

Organizational Affiliation

Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom. Stacey.Southall@icr.ac.uk

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P75804
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain J [auth A] SDF format, chain Q [auth A] SDF format, chain W [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain R [auth B]	C [auth A], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.183
R-Value Work: 0.149
R-Value Observed: 0.148
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-08-08

Deposition Author(s):

Revision History (Full details and data files)

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