3WIC

Structure of a substrate/cofactor-unbound glucose dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium.

Kanoh, Y.Uehara, S.Iwata, H.Yoneda, K.Ohshima, T.Sakuraba, H.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1271-1280

  • DOI: 10.1107/S1399004714002363
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium (tvGlcDH) is highly active towards D-glucose and D-galactose, but does not utilize aldopentoses such as D-xylose as substrates. In the present study, the crystal structu ...

    Glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium (tvGlcDH) is highly active towards D-glucose and D-galactose, but does not utilize aldopentoses such as D-xylose as substrates. In the present study, the crystal structures of substrate/cofactor-free tvGlcDH and of a tvGlcDH T277F mutant in a binary complex with NADP and in a ternary complex with D-glucose and nicotinic acid adenine dinucleotide phosphate, an NADP analogue, were determined at resolutions of 2.6, 2.25 and 2.33 Å, respectively. The overall structure of each monomer showed notable similarity to that of the enzyme from Sulfolobus solfataricus (ssGlcDH-1), which accepts a broad range of C5 and C6 sugars as substrates. However, the amino-acid residues of tvGlcDH involved in substrate binding markedly differed from those of ssGlcDH-1. Structural comparison revealed that a decreased number of interactions between the C3-hydroxyl group of the sugar and the enzyme are likely to be responsible for the lack of reactivity of tvGlcDH towards D-xylose.


    Organizational Affiliation

    Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucose 1-dehydrogenaseA, B, C, D361Thermoplasma volcanium GSS1Mutation(s): 0 
Gene Names: gdhTV1048TVG1073292
EC: 1.1.1.47
Find proteins for Q979W2 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1))
Explore Q979W2 
Go to UniProtKB:  Q979W2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download CCD File 
A, B, C, D
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

Download CCD File 
A, B, C, D
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.088α = 90
b = 122.175β = 109.92
c = 87.428γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2019-12-25
    Changes: Database references