The crystal structure of 6-phospho-beta-glucosidase from Streptococcus mutans UA159 in complex with beta-D-glucose-6-phosphate.

Experimental Data Snapshot

  • Resolution: 1.48 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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This is version 1.3 of the entry. See complete history


GH1-family 6-P-beta-glucosidases from human microbiome lactic acid bacteria.

Michalska, K.Tan, K.Li, H.Hatzos-Skintges, C.Bearden, J.Babnigg, G.Joachimiak, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 451-463

  • DOI: https://doi.org/10.1107/S0907444912049608
  • Primary Citation of Related Structures:  
    3QOM, 4F66, 4F79, 4GPN, 4GZE

  • PubMed Abstract: 

    In lactic acid bacteria and other bacteria, carbohydrate uptake is mostly governed by phosphoenolpyruvate-dependent phosphotransferase systems (PTSs). PTS-dependent translocation through the cell membrane is coupled with phosphorylation of the incoming sugar. After translocation through the bacterial membrane, the β-glycosidic bond in 6'-P-β-glucoside is cleaved, releasing 6-P-β-glucose and the respective aglycon. This reaction is catalyzed by 6-P-β-glucosidases, which belong to two glycoside hydrolase (GH) families: GH1 and GH4. Here, the high-resolution crystal structures of GH1 6-P-β-glucosidases from Lactobacillus plantarum (LpPbg1) and Streptococcus mutans (SmBgl) and their complexes with ligands are reported. Both enzymes show hydrolytic activity towards 6'-P-β-glucosides. The LpPbg1 structure has been determined in an apo form as well as in a complex with phosphate and a glucose molecule corresponding to the aglycon molecule. The S. mutans homolog contains a sulfate ion in the phosphate-dedicated subcavity. SmBgl was also crystallized in the presence of the reaction product 6-P-β-glucose. For a mutated variant of the S. mutans enzyme (E375Q), the structure of a 6'-P-salicin complex has also been determined. The presence of natural ligands enabled the definition of the structural elements that are responsible for substrate recognition during catalysis.

  • Organizational Affiliation

    Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative phospho-beta-glucosidase
A, B
480Streptococcus mutansMutation(s): 0 
Gene Names: bglSMU_1601
Find proteins for Q8DT00 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q8DT00 
Go to UniProtKB:  Q8DT00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DT00
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BG6

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C6 H13 O9 P
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
C2 H6 O2
Query on FMT

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
C H2 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.48 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.665α = 90
b = 92.449β = 101.32
c = 94.351γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary