4E13 | pdb_00004e13

Substrate-directed dual catalysis of dicarbonyl compounds by diketoreductase

• PDB DOI: https://doi.org/10.2210/pdb4E13/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baylyi
• Mutation(s): No 


• Deposited: 2012-03-05 Released: 2012-11-14 
• Deposition Author(s): Lu, M., White, M.A., Huang, Y., Wu, X., Liu, N., Cheng, X., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

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

• PubMed: 23073461 
• DOI: https://doi.org/10.1039/c2cc36334h
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.63 kDa 
• Atom Count: 2,259 
• Modeled Residue Count: 283 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diketoreductase	A	283	Acinetobacter baylyi	Mutation(s): 0
UniProt
Find proteins for B1P3E1 (Acinetobacter baylyi) Explore B1P3E1  Go to UniProtKB:  B1P3E1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
1PE	G [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	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: 2.08 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.75	α = 90
b = 100.75	β = 90
c = 132.09	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
CNS	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Lu, M., White, M.A., Huang, Y., Wu, X., Liu, N., Cheng, X., Chen, Y.

Revision History  

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