4IPL | pdb_00004ipl

The crystal structure of 6-phospho-beta-glucosidase BglA-2 from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the substrate specificity of a 6-phospho-&[beta]-glucosidase BglA-2 from Streptococcus pneumoniae TIGR4

Yu, W.L.Jiang, Y.L.Pikis, A.Cheng, W.Bai, X.H.Ren, Y.M.Thompson, J.Zhou, C.Z.Chen, Y.

(2013) J Biological Chem 288: 14949-14958

  • DOI: https://doi.org/10.1074/jbc.M113.454751
  • Primary Citation of Related Structures:  
    4IPL, 4IPN

  • PubMed Abstract: 

    The 6-phospho-β-glucosidase BglA-2 (EC 3.2.1.86) from glycoside hydrolase family 1 (GH-1) catalyzes the hydrolysis of β-1,4-linked cellobiose 6-phosphate (cellobiose-6'P) to yield glucose and glucose 6-phosphate. Both reaction products are further metabolized by the energy-generating glycolytic pathway. Here, we present the first crystal structures of the apo and complex forms of BglA-2 with thiocellobiose-6'P (a non-metabolizable analog of cellobiose-6'P) at 2.0 and 2.4 Å resolution, respectively. Similar to other GH-1 enzymes, the overall structure of BglA-2 from Streptococcus pneumoniae adopts a typical (β/α)8 TIM-barrel, with the active site located at the center of the convex surface of the β-barrel. Structural analyses, in combination with enzymatic data obtained from site-directed mutant proteins, suggest that three aromatic residues, Tyr(126), Tyr(303), and Trp(338), at subsite +1 of BglA-2 determine substrate specificity with respect to 1,4-linked 6-phospho-β-glucosides. Moreover, three additional residues, Ser(424), Lys(430), and Tyr(432) of BglA-2, were found to play important roles in the hydrolytic selectivity toward phosphorylated rather than non-phosphorylated compounds. Comparative structural analysis suggests that a tryptophan versus a methionine/alanine residue at subsite -1 may contribute to the catalytic and substrate selectivity with respect to structurally similar 6-phospho-β-galactosidases and 6-phospho-β-glucosidases assigned to the GH-1 family.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phospho-beta-glucosidase
A, B
487Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: bglA-2SP_0578
EC: 3.2.1.86
UniProt
Find proteins for A0A0H2UP35 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2UP35 
Go to UniProtKB:  A0A0H2UP35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UP35
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.28α = 90
b = 65.35β = 133.38
c = 126.69γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations