7NZP | pdb_00007nzp

D-lyxose isomerase from the hyperthermophilic archaeon Thermofilum sp complexed with D-fructose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.184 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.3389/fbioe.2021.711487
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 48.45 kDa 
  • Atom Count: 3,522 
  • Modeled Residue Count: 365 
  • Deposited Residue Count: 408 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-lyxose/D-mannose family sugar isomeraseA [auth AAA],
B [auth BBB]
204Thermofilum sp. ex4484_79Mutation(s): 0 
Gene Names: B6U94_07925
EC: 5.3.1.15
UniProt
Find proteins for A0A256XLS3 (Thermofilum sp. (strain ex4484_79))
Explore A0A256XLS3 
Go to UniProtKB:  A0A256XLS3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A256XLS3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FRU
(Subject of Investigation/LOI)

Query on FRU



Download:Ideal Coordinates CCD File
C [auth AAA],
H [auth BBB]
beta-D-fructofuranose
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth AAA],
E [auth AAA],
F [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
G [auth AAA],
I [auth BBB]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.958α = 90
b = 86.647β = 112.274
c = 53.837γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary