1UP6

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


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


Literature

An Unusual Mechanism of Glycoside Hydrolysis Involving Redox and Elimination Steps by a Family 4 Beta-Glycosidase from Thermotoga Maritima.

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

(2004) J Am Chem Soc 126: 8354

  • DOI: 10.1021/ja047632w
  • Primary Citation of Related Structures:  
    1UP6

  • PubMed Abstract: 

    • Among the numerous well-characterized families of glycosidases, family 4 appears to be the anomaly, requiring both catalytic NAD+ and a divalent metal for activity. The unusual cofactor requirement prompted the proposal of a mechanism involving key NAD+-mediated redox steps as well as elimination of the glycosidic oxygen ...

    Among the numerous well-characterized families of glycosidases, family 4 appears to be the anomaly, requiring both catalytic NAD+ and a divalent metal for activity. The unusual cofactor requirement prompted the proposal of a mechanism involving key NAD+-mediated redox steps as well as elimination of the glycosidic oxygen. Primary kinetic isotope effects for the 2- and 3-deutero substrate analogues, isotopic exchange with solvent, and structural analysis of a 6-phospho-beta-glucosidase, BglT (E.C. 3.2.1.6), provided evidence in support of the proposed mechanism, which has striking resemblances to that of the sugar dehydratases. Furthermore, analysis of the stereochemical outcome indicated that family 4 enzymes are retaining glycosidases.

    Organizational Affiliation: 

    Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-PHOSPHO-BETA-GLUCOSIDASE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
416Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: bglT, TM_1281
EC: 3.2.1.6 (PDB Primary Data), 3.2.1.86 (UniProt)
UniProt
Find proteins for Q9X108 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X108 
Go to UniProtKB:  Q9X108
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X108
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
I [auth A],
O [auth C],
T [auth G]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
G6P
Query on G6P
Download Ideal Coordinates CCD File 
K [auth A],
Q [auth C]		6-O-phosphono-alpha-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
N [auth B],
R [auth D],
S [auth E],
V [auth G]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
J [auth A],
L [auth A],
M [auth A],
P [auth C],
U [auth G]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.438α = 90
b = 179.438β = 90
c = 282.911γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-02
    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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary