4KTR | pdb_00004ktr

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 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4KTR

This is version 1.4 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 Biological Chem 289: 18067-18075

  • DOI: https://doi.org/10.1074/jbc.M114.573212
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 708.73 kDa 
  • Atom Count: 51,264 
  • Modeled Residue Count: 6,090 
  • Deposited Residue Count: 6,152 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 65 central catalytic
A, B, C, D, E
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / 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
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
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
P6G

Query on P6G



Download:Ideal Coordinates CCD File
EB [auth E],
N [auth A]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
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
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
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
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
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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
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
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Structure summary