4E12

Substrate-directed dual catalysis of dicarbonyl compounds by diketoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dual catalysis mode for the dicarbonyl reduction catalyzed by diketoreductase

Lu, M.Huang, Y.White, M.A.Wu, X.Liu, N.Cheng, X.Chen, Y.

(2012) Chem Commun (Camb) 48: 11352-11354

  • DOI: https://doi.org/10.1039/c2cc36334h
  • Primary Citation of Related Structures:  
    4DYD, 4E12, 4E13

  • PubMed Abstract: 

    Diketoreductase catalyzes a two-step bioreduction on a dicarbonyl substrate through a novel dual catalysis mode, in which random hydride attack simultaneously forms two mono-carbonyl intermediates, and subsequently distinct catalytic sites are responsible for the reductions of respective carbonyl group of the intermediates to yield the final dihydroxy product.


  • Organizational Affiliation

    Laboratory of Chemical Biology, China Pharmaceutical University, 24 Tongjia Street, Nanjing, Jiangsu Province 210009, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diketoreductase283Acinetobacter baylyiMutation(s): 0 
UniProt
Find proteins for B1P3E1 (Acinetobacter baylyi)
Explore B1P3E1 
Go to UniProtKB:  B1P3E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1P3E1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
G [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.56α = 90
b = 99.56β = 90
c = 131.86γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
CNSrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description