3QOM

Crystal structure of 6-phospho-beta-glucosidase from Lactobacillus plantarum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.118 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phospho-beta-glucosidase481Lactiplantibacillus plantarumMutation(s): 0 
Gene Names: pbg1lp_0440
EC: 3.2.1.86
UniProt
Find proteins for F9UU25 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore F9UU25 
Go to UniProtKB:  F9UU25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9UU25
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.647α = 90
b = 150.647β = 90
c = 95.9γ = 120
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-07-02
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary