1UP7

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.4 Angstrom resolution in the tetragonal form with NAD and glucose-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Nad+ and Metal-Ion Dependent Hydrolysis by Family 4 Glycosidases: Structural Insight Into Specificity for Phospho-Beta-D-Glucosides

Varrot, A.Yip, V.L.Li, Y.Rajan, S.S.Yang, X.Anderson, W.F.Thompson, J.Withers, S.G.Davies, G.J.

(2005) J.Mol.Biol. 346: 423

  • DOI: 10.1016/j.jmb.2004.11.058
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The import of disaccharides by many bacteria is achieved through their simultaneous translocation and phosphorylation by the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). The imported phospho-disaccharides are, in some cases, sub ...

    The import of disaccharides by many bacteria is achieved through their simultaneous translocation and phosphorylation by the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). The imported phospho-disaccharides are, in some cases, subsequently hydrolyzed by members of the unusual glycoside hydrolase family GH4. The GH4 enzymes, occasionally found also in bacteria such as Thermotoga maritima that do not utilise a PEP-PTS system, require both NAD(+) and Mn(2+) for catalysis. A further curiosity of this family is that closely related enzymes may show specificity for either alpha-d- or beta-d-glycosides. Here, we present, for the first time, the three-dimensional structure (using single-wavelength anomalous dispersion methods, harnessing extensive non-crystallographic symmetry) of the 6-phospho-beta-glycosidase, BglT, from T.maritima in native and complexed (NAD(+) and Glc6P) forms. Comparison of the active-center structure with that of the 6-phospho-alpha-glucosidase GlvA from Bacillus subtilis reveals a striking degree of structural similarity that, in light of previous kinetic isotope effect data, allows the postulation of a common reaction mechanism for both alpha and beta-glycosidases. Given that the "chemistry" occurs primarily on the glycone sugar and features no nucleophilic attack on the intact disaccharide substrate, modulation of anomeric specificity for alpha and beta-linkages is accommodated through comparatively minor structural changes.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-PHOSPHO-BETA-GLUCOSIDASE
A, B, C, D, E, F, G, H
417Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: bglT
EC: 3.2.1.86
Find proteins for Q9X108 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X108
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
G6P
Query on G6P

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ALPHA-D-GLUCOSE-6-PHOSPHATE
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 178.132α = 90.00
b = 178.132β = 90.00
c = 278.927γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2012-06-20
    Type: Other
  • Version 1.3: 2016-12-28
    Type: Data collection, Structure summary