1IWP

Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.

Yamanishi, M.Yunoki, M.Tobimatsu, T.Sato, H.Matsui, J.Dokiya, A.Iuchi, Y.Oe, K.Suto, K.Shibata, N.Morimoto, Y.Yasuoka, N.Toraya, T.

(2002) Eur.J.Biochem. 269: 4484-4494


  • PubMed Abstract: 
  • Recombinant glycerol dehydratase of Klebsiella pneumoniae was purified to homogeneity. The subunit composition of the enzyme was most probably alpha 2 beta 2 gamma 2. When (R)- and (S)-propane-1,2-diols were used independently as substrates, the rate ...

    Recombinant glycerol dehydratase of Klebsiella pneumoniae was purified to homogeneity. The subunit composition of the enzyme was most probably alpha 2 beta 2 gamma 2. When (R)- and (S)-propane-1,2-diols were used independently as substrates, the rate with the (R)-enantiomer was 2.5 times faster than that with the (S)-isomer. In contrast to diol dehydratase, an isofunctional enzyme, the affinity of the enzyme for the (S)-isomer was essentially the same or only slightly higher than that for the (R)-isomer (Km(R)/Km(S) = 1.5). The crystal structure of glycerol dehydratase in complex with cyanocobalamin and propane-1,2-diol was determined at 2.1 A resolution. The enzyme exists as a dimer of the alpha beta gamma heterotrimer. Cobalamin is bound at the interface between the alpha and beta subunits in the so-called 'base-on' mode with 5,6-dimethylbenzimidazole of the nucleotide moiety coordinating to the cobalt atom. The electron density of the cyano group was almost unobservable, suggesting that the cyanocobalamin was reduced to cob(II)alamin by X-ray irradiation. The active site is in a (beta/alpha)8 barrel that was formed by a central region of the alpha subunit. The substrate propane-1,2-diol and essential cofactor K+ are bound inside the (beta/alpha)8 barrel above the corrin ring of cobalamin. K+ is hepta-coordinated by the two hydroxyls of the substrate and five oxygen atoms from the active-site residues. These structural features are quite similar to those of diol dehydratase. A closer contact between the alpha and beta subunits in glycerol dehydratase may be reminiscent of the higher affinity of the enzyme for adenosylcobalamin than that of diol dehydratase. Although racemic propane-1,2-diol was used for crystallization, the substrate bound to glycerol dehydratase was assigned to the (R)-isomer. This is in clear contrast to diol dehydratase and accounts for the difference between the two enzymes in the susceptibility of suicide inactivation by glycerol.


    Organizational Affiliation

    Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Okayama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol Dehydratase Alpha subunit
A, L
555Klebsiella pneumoniaeGene Names: dhaB1 (dhaB, gldA, pduC)
EC: 4.2.1.30
Find proteins for Q59476 (Klebsiella pneumoniae)
Go to UniProtKB:  Q59476
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glycerol Dehydratase Beta subunit
B, E
194Klebsiella pneumoniaeGene Names: gldB
EC: 4.2.1.30
Find proteins for O08505 (Klebsiella pneumoniae)
Go to UniProtKB:  O08505
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Glycerol Dehydratase Gamma subunit
G, M
141Klebsiella pneumoniaeGene Names: dhaB3 (dhaE, gldC, pduE)
EC: 4.2.1.30
Find proteins for Q59475 (Klebsiella pneumoniae)
Go to UniProtKB:  Q59475
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, L
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
B12
Query on B12

Download SDF File 
Download CCD File 
B, E
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
PGO
Query on PGO

Download SDF File 
Download CCD File 
A, L
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.380α = 90.00
b = 108.223β = 96.75
c = 113.141γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
MOSFLMdata reduction
CCP4data scaling
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-10-24
    Type: Non-polymer description