3VNM

Crystal structures of D-Psicose 3-epimerase with D-sorbose from Clostridium cellulolyticum H10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 

Starting Model: experimental
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Literature

Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars.

Chan, H.C.Zhu, Y.Hu, Y.Ko, T.P.Huang, C.H.Ren, F.Chen, C.C.Ma, Y.Guo, R.T.Sun, Y.

(2012) Protein Cell 3: 123-131

  • DOI: https://doi.org/10.1007/s13238-012-2026-5
  • Primary Citation of Related Structures:  
    3VNI, 3VNJ, 3VNK, 3VNL, 3VNM

  • PubMed Abstract: 

    D-psicose 3-epimerase (DPEase) is demonstrated to be useful in the bioproduction of D-psicose, a rare hexose sugar, from D-fructose, found plenty in nature. Clostridium cellulolyticum H10 has recently been identified as a DPEase that can epimerize D-fructose to yield D-psicose with a much higher conversion rate when compared with the conventionally used DTEase. In this study, the crystal structure of the C. cellulolyticum DPEase was determined. The enzyme assembles into a tetramer and each subunit shows a (β/α)(8) TIM barrel fold with a Mn(2+) metal ion in the active site. Additional crystal structures of the enzyme in complex with substrates/products (D-psicose, D-fructose, D-tagatose and D-sorbose) were also determined. From the complex structures of C. cellulolyticum DPEase with D-psicose and D-fructose, the enzyme has much more interactions with D-psicose than D-fructose by forming more hydrogen bonds between the substrate and the active site residues. Accordingly, based on these ketohexose-bound complex structures, a C3-O3 proton-exchange mechanism for the conversion between D-psicose and D-fructose is proposed here. These results provide a clear idea for the deprotonation/protonation roles of E150 and E244 in catalysis.


  • Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase domain protein TIM barrel
A, B, C, D
293Ruminiclostridium cellulolyticum H10Mutation(s): 0 
Gene Names: Ccel_0941
EC: 5.1.3.30
UniProt
Find proteins for B8I944 (Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10))
Explore B8I944 
Go to UniProtKB:  B8I944
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8I944
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SDD
Query on SDD

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
O [auth D]
D-sorbose
C6 H12 O6
BJHIKXHVCXFQLS-PYWDMBMJSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.924α = 90
b = 115.225β = 105.73
c = 91.614γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description