4KTR

Crystal structure of 2-O-alpha-glucosylglycerol phosphorylase in complex with isofagomine and glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for reversible phosphorolysis and hydrolysis reactions of 2-O-alpha-glucosylglycerol phosphorylase

Touhara, K.K.Nihira, T.Kitaoka, M.Nakai, H.Fushinobu, S.

(2014) J Biol Chem 289: 18067-18075

  • DOI: 10.1074/jbc.M114.573212
  • Primary Citation of Related Structures:  
    4KTP, 4KTR

  • PubMed Abstract: 
  • 2-O-α-Glucosylglycerol phosphorylase (GGP) from Bacillus selenitireducens catalyzes both the reversible phosphorolysis of 2-O-α-glucosylglycerol (GG) and the hydrolysis of β-d-glucose 1-phosphate (βGlc1P). GGP belongs to the glycoside hydrolase (GH) family 65 and can efficiently and specifically produce GG ...

    2-O-α-Glucosylglycerol phosphorylase (GGP) from Bacillus selenitireducens catalyzes both the reversible phosphorolysis of 2-O-α-glucosylglycerol (GG) and the hydrolysis of β-d-glucose 1-phosphate (βGlc1P). GGP belongs to the glycoside hydrolase (GH) family 65 and can efficiently and specifically produce GG. However, its structural basis has remained unclear. In this study, the crystal structures of GGP complexed with glucose and the glucose analog isofagomine and glycerol were determined. Subsite -1 of GGP is similar to those of other GH65 enzymes, maltose phosphorylase and kojibiose phosphorylase, whereas subsite +1 is largely different and is well designed for GG recognition. An automated docking analysis was performed to complement these crystal structures, βGlc1P being docked at an appropriate position. To investigate the importance of residues at subsite +1 in the bifunctionality of GGP, we constructed mutants at these residues. Y327F and K587A did not show detectable activities for either reverse phosphorolysis or βGlc1P hydrolysis. Y572F also showed significantly reduced activities for both of these reactions. In contrast, W381F showed significantly reduced reverse phosphorolytic activity but retained βGlc1P hydrolysis. The mode of substrate recognition and the reaction mechanisms of GGP were proposed based on these analyses. Specifically, an extensive hydrogen bond network formed by Tyr-327, Tyr-572, Lys-587, and water molecules contributes to fixing the acceptor molecule in both reverse phosphorolysis (glycerol) and βGlc1P hydrolysis (water) for a glycosyl transfer reaction. This study will contribute to the development of a large scale production system of GG by facilitating the rational engineering of GGP.


    Organizational Affiliation

    From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, asfushi@mail.ecc.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoside hydrolase family 65 central catalytic
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
769[Bacillus] selenitireducens MLS10Mutation(s): 1 
Gene Names: Bsel_2816
EC: 2.4.1 (PDB Primary Data), 2.4.1.332 (UniProt)
UniProt
Find proteins for D6XZ22 (Bacillus selenitireducens (strain ATCC 700615 / DSM 15326 / MLS10))
Explore D6XZ22 
Go to UniProtKB:  D6XZ22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6XZ22
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE5
Query on PE5

Download Ideal Coordinates CCD File 
DC [auth H]3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
 Ligand Interaction
PE4
Query on PE4

Download Ideal Coordinates CCD File 
IA [auth C]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
7PE
Query on 7PE

Download Ideal Coordinates CCD File 
VA [auth D],
W [auth B]
2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
EB [auth E],
N [auth A]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
DB [auth E],
EA [auth C],
J [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
MB [auth F],
QA [auth D],
V [auth B],
YB [auth H]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
KA [auth C],
PB [auth F],
T [auth A],
UB [auth G]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
IFM
Query on IFM

Download Ideal Coordinates CCD File 
CB [auth E],
I [auth A],
KB [auth F],
OA [auth D],
QB [auth G],
CB [auth E],
I [auth A],
KB [auth F],
OA [auth D],
QB [auth G],
WB [auth H]
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B],
AC [auth H],
BA [auth B],
BC [auth H],
CA [auth B],
AA [auth B],
AC [auth H],
BA [auth B],
BC [auth H],
CA [auth B],
CC [auth H],
FA [auth C],
FB [auth E],
GA [auth C],
GB [auth E],
HA [auth C],
HB [auth E],
IB [auth E],
JA [auth C],
K [auth A],
L [auth A],
LA [auth C],
LB [auth F],
M [auth A],
MA [auth C],
NB [auth F],
O [auth A],
OB [auth F],
P [auth A],
PA [auth D],
Q [auth A],
R [auth A],
RA [auth D],
RB [auth G],
S [auth A],
SA [auth D],
SB [auth G],
TA [auth D],
TB [auth G],
UA [auth D],
WA [auth D],
X [auth B],
XA [auth D],
XB [auth H],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D],
ZB [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth D],
BB [auth D],
DA [auth B],
JB [auth E],
NA [auth C],
AB [auth D],
BB [auth D],
DA [auth B],
JB [auth E],
NA [auth C],
U [auth A],
VB [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.003α = 90
b = 263.213β = 105.45
c = 138.793γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2015-08-12
    Changes: Non-polymer description