7NZO

D-lyxose isomerasefrom the hyperthermophilic archaeon Thermofilum sp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 

wwPDB Validation 

Currently 7NZO does not have a validation slider image.


This is version 1.0 of the entry. See complete history


Literature

Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp.

De Rose, S.A.Kuprat, T.Isupov, M.N.Reinhardt, A.Schonheit, P.Littlechild, J.A.

(2021) Front Bioeng Biotechnol 9: 711487-711487

  • DOI: 10.3389/fbioe.2021.711487
  • Primary Citation of Related Structures:  
    7NZO, 7NZP, 7NZQ

  • PubMed Abstract: 
  • A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases ...

    A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases. This is the most thermoactive and thermostable lyxose isomerase reported to date, showing activity above 95°C and retaining 60% of its activity after 60 min incubation at 80°C. This lyxose isomerase is stable in the presence of 50% (v/v) of solvents ethanol, methanol, acetonitrile and DMSO. The crystal structure of the enzyme has been resolved to 1.4-1.7 A. resolution in the ligand-free form and in complexes with both of the slowly reacting sugar substrates mannose and fructose. This thermophilic lyxose isomerase is stabilised by a disulfide bond between the two monomers of the dimeric enzyme and increased hydrophobicity at the dimer interface. These overall properties of high substrate specificity, thermostability and solvent tolerance make this lyxose isomerase enzyme a good candidate for potential industrial applications.


    Organizational Affiliation

    The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-lyxose/D-mannose family sugar isomeraseA [auth AAA], B [auth BBB]204Thermofilum sp. ex4484_79Mutation(s): 0 
Gene Names: B6U94_07925
UniProt
Find proteins for A0A256XLS3 (Thermofilum sp. ex4484_79)
Explore A0A256XLS3 
Go to UniProtKB:  A0A256XLS3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth AAA] , D [auth AAA] , E [auth AAA] , F [auth AAA] , G [auth AAA] , H [auth AAA] , J [auth BBB] , K [auth BBB] , 
C [auth AAA],  D [auth AAA],  E [auth AAA],  F [auth AAA],  G [auth AAA],  H [auth AAA],  J [auth BBB],  K [auth BBB],  L [auth BBB],  M [auth BBB],  N [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
I [auth AAA], O [auth BBB]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.77α = 90
b = 86.91β = 112.93
c = 54.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing

Structure Validation

Currently 7NZO does not have a validation slider image.




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany031B0271

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release