7CJ9

Crystal structure of N-terminal His-tagged D-allulose 3-epimerase from Methylomonas sp. with additional C-terminal residues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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, C, D, E
A, B, C, D, E, F, G, H
316Methylomonas sp. DH-1Mutation(s): 3 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
BA [auth E]
GA [auth F]
JA [auth G]
K [auth A]
MA [auth H]
BA [auth E],
GA [auth F],
JA [auth G],
K [auth A],
MA [auth H],
N [auth B],
T [auth C],
X [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
FUD (Subject of Investigation/LOI)
Query on FUD

Download Ideal Coordinates CCD File 
AA [auth E]
FA [auth F]
IA [auth G]
J [auth A]
LA [auth H]
AA [auth E],
FA [auth F],
IA [auth G],
J [auth A],
LA [auth H],
M [auth B],
S [auth C],
W [auth D]
D-fructose
C6 H12 O6
BJHIKXHVCXFQLS-UYFOZJQFSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
O [auth C]
P [auth C]
Q [auth C]
CA [auth F],
DA [auth F],
O [auth C],
P [auth C],
Q [auth C],
U [auth D],
Y [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
EA [auth F]
HA [auth G]
I [auth A]
KA [auth H]
L [auth B]
EA [auth F],
HA [auth G],
I [auth A],
KA [auth H],
L [auth B],
R [auth C],
V [auth D],
Z [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.43α = 87.67
b = 92.77β = 98.64
c = 93.78γ = 115.6
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
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: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description