3BFJ

Crystal structure analysis of 1,3-propanediol oxidoreductase

• PDB DOI:  https://doi.org/10.2210/pdb3BFJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-21 Released: 2008-11-25 
• Deposition Author(s): Marcal, D., Enguita, F.J., Carrondo, M.A., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Literature

1,3-propanediol dehydrogenase from Klebsiella pneumoniae: decameric quaternary structure and possible subunit cooperativity

Marcal, D., Rego, A.T., Carrondo, M.A., Enguita, F.J.

(2009) J Bacteriol 191: 1143-1151

• PubMed: 19011020 
• DOI: https://doi.org/10.1128/JB.01077-08
• Primary Citation of Related Structures:  
  3BFJ


• PubMed Abstract: 
  

Klebsiella pneumoniae is a nosocomial pathogen frequently isolated from opportunistic infections, especially in clinical environments. In spite of its potential pathogenicity, this microorganism has several metabolic potentials that could be used in biotechnology applications. K. pneumoniae is able to metabolize glycerol as a sole source of carbon and energy. 1,3-Propanediol dehydrogenase is the core of the metabolic pathway for the use of glycerol. We have determined the crystallographic structure of 1,3-propanediol dehydrogenase, a type III Fe-NAD-dependent alcohol dehydrogenase, at 2.7-A resolution. The structure of the enzyme monomer is closely related to that of other alcohol dehydrogenases. The overall arrangement of the enzyme showed a decameric structure, formed by a pentamer of dimers, which is the catalytic form of the enzyme. Dimers are associated by strong ionic interactions that are responsible for the highly stable in vivo packing of the enzyme. Kinetic properties of the enzyme as determined in the article would suggest that this decameric arrangement is related to the cooperativity between monomers.

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Organizational Affiliation: 

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 generated by PISA (software)

Biological Assembly 9  

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

Biological assembly 9 generated by PISA (software)

Biological Assembly 10  

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

Biological assembly 10 generated by PISA (software)

Biological Assembly 11  

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

Biological assembly 11 generated by PISA (software)

Biological Assembly 12  

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

Biological assembly 12 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 832.89 kDa 
• Atom Count: 58,348 
• Modelled Residue Count: 7,640 
• Deposited Residue Count: 7,740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,3-propanediol oxidoreductase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	387	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: dhaT, dhaT_2, NCTC3279_03835 EC: 1.1.1.202
UniProt
Find proteins for Q7WRJ3 (Klebsiella pneumoniae) Explore Q7WRJ3  Go to UniProtKB:  Q7WRJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	AA [auth G], BA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], KA [auth Q], LA [auth R], MA [auth S], NA [auth T], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.251 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.937	α = 90
b = 226.611	β = 92.91
c = 232.627	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Marcal, D., Enguita, F.J., Carrondo, M.A., Structural Proteomics in Europe (SPINE)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary