Crystal structure of a 6-phospho-beta-galactosidase from Bacillus licheniformis

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Differences in Gluco and Galacto Substrate-Binding Interactions in a Dual 6P beta-Glucosidase/6P beta-Galactosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis .

Veldman, W.Liberato, M.V.Souza, V.P.Almeida, V.M.Marana, S.R.Tastan Bishop, O.Polikarpov, I.

(2021) J Chem Inf Model 61: 4554-4570

  • DOI: https://doi.org/10.1021/acs.jcim.1c00413
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bacterial glycoside hydrolase 1 (GH1) enzymes with 6-phospho-β-galactosidase and 6-phospho-β-glucosidase activities have the important task of releasing phosphorylated and nonphosphorylated monosaccharides into the cytoplasm. Curiously, dual 6-phospho-β-galactosidase/6-phospho-β-glucosidase (dual-phospho) enzymes have broad specificity and are able to hydrolyze galacto- and gluco-derived substrates. This study investigates the structure and substrate specificity of a GH family 1 enzyme from Bacillus licheniformis , hereafter known as Bl BglC. The enzyme structure has been solved, and sequence analysis, molecular dynamics simulations, and binding free energy calculations offered evidence of dual-phospho activity. Both test ligands p -nitrophenyl-β-d-galactoside-6-phosphate (PNP6Pgal) and p -nitrophenyl-β-d-glucoside-6-phosphate (PNP6Pglc) demonstrated strong binding to Bl BglC although the pose and interactions of the PNP6Pglc triplicates were slightly more consistent. Interestingly, known specificity-inducing residues, Gln23 and Trp433, bind strongly to the ligand O3 hydroxyl group in the PNP6Pgal- Bl BglC complex and to the ligand O4 hydroxyl group in the PNP6Pglc- Bl BglC complex. Additionally, the Bl BglC-His124 residue is a major contributor of hydrogen bonds to the PNP6Pgal O3 hydroxyl group but does not form any hydrogen bonds with PNP6Pglc. On the other hand, Bl BglC residues Tyr173, Tyr301, Gln302, and Thr321 form hydrogen bonds with PNP6Pglc but not PNP6Pgal. These findings provide important details of the broad specificity of dual-phospho activity GH1 enzymes.

  • Organizational Affiliation

    Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
480Bacillus licheniformisMutation(s): 0 
Gene Names: bglC1
Find proteins for Q65NL9 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46))
Explore Q65NL9 
Go to UniProtKB:  Q65NL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65NL9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.988α = 90
b = 71.38β = 100.94
c = 169.29γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2015/13684-0
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil423693/2016-6
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil303988/2016-9

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description