4HHM

Crystal structure of a mutant, G219A, of Glucose Isomerase from Streptomyces sp. SK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Identification of critical residues for the activity and thermostability of Streptomyces sp. SK glucose isomerase.

Ben Hlima, H.Bejar, S.Riguet, J.Haser, R.Aghajari, N.

(2013) Appl Microbiol Biotechnol 97: 9715-9726

  • DOI: https://doi.org/10.1007/s00253-013-4784-2
  • Primary Citation of Related Structures:  
    4HHL, 4HHM

  • PubMed Abstract: 

    The role of residue 219 in the physicochemical properties of D-glucose isomerase from Streptomyces sp. SK strain (SKGI) was investigated by site-directed mutagenesis and structural studies. Mutants G219A, G219N, and G219F were generated and characterized. Comparative studies of their physicochemical properties with those of the wild-type enzyme highlighted that mutant G219A displayed increased specific activity and thermal stability compared to that of the wild-type enzyme, while for G219N and G219F, these properties were considerably decreased. A double mutant, SKGI F53L/G219A, displayed a higher optimal temperature and a higher catalytic efficiency than both the G219A mutant and the wild-type enzyme and showed a half-life time of about 150 min at 85 °C as compared to 50 min for wild-type SKGI. Crystal structures of SKGI wild-type and G219A enzymes were solved to 1.73 and 2.15 Å, respectively, and showed that the polypeptide chain folds into two structural domains. The larger domain consists of a (β/α)8 unit, and the smaller domain forms a loop of α helices. Detailed analyses of the three-dimensional structures highlighted minor but important changes in the active site region as compared to that of the wild-type enzyme leading to a displacement of both metal ions, and in particular that in site M2. The structural analyses moreover revealed how the substitution of G219 by an alanine plays a crucial role in improving the thermostability of the mutant enzyme.


  • Organizational Affiliation

    Laboratoire de Micro-organismes et de Biomolécules, Centre de Biotechnologie de Sfax, Université de Sfax, BP "1177", 3018, Sfax, Tunisia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase
A, B, C, D, E
A, B, C, D, E, F, G, H
388Streptomyces sp. SKMutation(s): 1 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for Q9ZAI3 (Streptomyces sp. SK)
Explore Q9ZAI3 
Go to UniProtKB:  Q9ZAI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZAI3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.5α = 90
b = 137.4β = 90.06
c = 136.6γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references
  • Version 1.3: 2013-11-13
    Changes: Database references
  • Version 1.4: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description