3BFJ | pdb_00003bfj

Crystal structure analysis of 1,3-propanediol oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.251 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3BFJ

This is version 1.3 of the entry. See complete history

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

  • DOI: https://doi.org/10.1128/JB.01077-08
  • Primary Citation 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.


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

Macromolecule Content 

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

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1,3-propanediol oxidoreductase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
387Klebsiella pneumoniaeMutation(s): 0 
Gene Names: dhaT
EC: 1.1.1.202
UniProt
Find proteins for Q59477 (Klebsiella pneumoniae)
Explore Q59477 
Go to UniProtKB:  Q59477
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59477
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE2

Query on FE2



Download:Ideal Coordinates CCD File
AA [auth G]
BA [auth H]
CA [auth I]
DA [auth J]
EA [auth K]
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 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.937α = 90
b = 226.611β = 92.91
c = 232.627γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description