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 

Starting Model: experimental
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This is version 1.2 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 11: 1621-1637

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

  • 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. 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 Escherichia 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

    Life Science Research Center and Faculty of Medicine, Kagawa University, Kita, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epimerase
A, B
294Methylomonas sp. DH-1Mutation(s): 0 
Gene Names: AYM39_05640
EC: 5.1.3.31
UniProt
Find proteins for A0A172U6X0 (Methylomonas sp. (strain DH-1))
Explore A0A172U6X0 
Go to UniProtKB:  A0A172U6X0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A172U6X0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BDF
Query on BDF

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

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

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

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description