4IPN

The complex structure of 6-phospho-beta-glucosidase BglA-2 with thiocellobiose-6P from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.411 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.174 

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.Biol.Chem. 288: 14949-14958

  • DOI: 10.1074/jbc.M113.454751
  • Primary Citation of Related Structures:  4IPL

  • 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 me ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phospho-beta-glucosidase
B, E
487Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Gene Names: bglA-2
EC: 3.2.1.86
Find proteins for A0A0H2UP35 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2UP35
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FT
Query on 1FT

Download SDF File 
Download CCD File 
B, E
4-S-(6-O-phosphono-alpha-L-idopyranosyl)-4-thio-beta-D-glucopyranose
thiocellobiose-6P
C12 H23 O13 P S
XGJJBBUPFWZKFA-GABYZZBISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1FTKd: 408700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.411 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.030α = 90.00
b = 66.650β = 136.33
c = 133.350γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
AMoREphasing
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary