7CJ5

Crystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with D-fructose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of a novel homodimeric L-ribulose 3-epimerase from Methylomonus sp.

Yoshida, H.Yoshihara, A.Kato, S.Mochizuki, S.Akimitsu, K.Izumori, K.Kamitori, S.

(2021) FEBS Open Bio 

  • DOI: 10.1002/2211-5463.13159
  • Primary Citation of Related Structures:  
    7CJ8, 7CJ9, 7CJ6, 7CJ7, 7CJ4, 7CJ5

  • PubMed Abstract: 
  • D-allulose has potential as a low calorie sweetener which can suppress fat accumulation. Several enzymes capable of D-allulose production have been isolated, including D-tagatose 3-epimerases. Here, we report the isolation of a novel protein from Methylomonas sp ...

    D-allulose has potential as a low calorie sweetener which can suppress fat accumulation. Several enzymes capable of D-allulose production have been isolated, including D-tagatose 3-epimerases. Here, we report the isolation of a novel protein from Methylomonas sp. expected to be a putative enzyme based on sequence similarity to ketose 3-epimerase. The synthesized gene encoding the deduced ketose 3-epimerase was expressed as a recombinant enzyme in E. coli, and it exhibited the highest enzymatic activity toward L-ribulose, followed by D-ribulose and D-allulose. The X-ray structure analysis of L-ribulose 3-epimerase from Methylomonas sp. (MetLRE) revealed a homodimeric enzyme, the first reported structure of dimeric L-ribulose 3-epimerase. The monomeric structure of MetLRE is similar to that of homotetrameric L-ribulose 3-epimerases, but the short C-terminal α-helix of MetLRE is unique and different from those of known L-ribulose 3 epimerases. The length of the C-terminal α-helix was thought to be involved in tetramerization and increasing stability; however, the addition of residues to MetLRE at the C-terminus did not lead to tetramer formation. MetLRE is the first dimeric L-ribulose 3-epimerase identified to exhibit high relative activity toward D-allulose.


    Organizational Affiliation

    International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EpimeraseA, B294Methylomonas sp. DH-1Mutation(s): 0 
Gene Names: AYM39_05640
Find proteins for A0A172U6X0 (Methylomonas sp. DH-1)
Explore A0A172U6X0 
Go to UniProtKB:  A0A172U6X0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUD
Query on FUD

Download Ideal Coordinates CCD File 
D [auth A], H [auth B]D-fructose
C6 H12 O6
BJHIKXHVCXFQLS-UYFOZJQFSA-N
 Ligand Interaction
BDF
Query on BDF

Download Ideal Coordinates CCD File 
F [auth A]beta-D-fructopyranose
C6 H12 O6
LKDRXBCSQODPBY-ARQDHWQXSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.42α = 90
b = 70.54β = 90
c = 140.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release