1DIO

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.

Shibata, N.Masuda, J.Tobimatsu, T.Toraya, T.Suto, K.Morimoto, Y.Yasuoka, N.

(1999) Structure Fold.Des. 7: 997-1008


  • PubMed Abstract: 
  • Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin (coenzyme B12) dependent conversion of 1,2-diols to the corresponding aldehydes. The reaction initiated by homolytic cleavage of the cobalt-carbon bond of the coenzyme proceeds by a r ...

    Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin (coenzyme B12) dependent conversion of 1,2-diols to the corresponding aldehydes. The reaction initiated by homolytic cleavage of the cobalt-carbon bond of the coenzyme proceeds by a radical mechanism. The enzyme is an alpha2beta2gamma2 heterooligomer and has an absolute requirement for a potassium ion for catalytic activity. The crystal structure analysis of a diol dehydratase-cyanocobalamin complex was carried out in order to help understand the mechanism of action of this enzyme.


    Organizational Affiliation

    Department of Life Science, Himeji Institute of Technology, Hyogo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DIOL DEHYDRATASE)
A, L
554Klebsiella oxytocaGene Names: pddA (pduC)
EC: 4.2.1.28
Find proteins for Q59470 (Klebsiella oxytoca)
Go to UniProtKB:  Q59470
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DIOL DEHYDRATASE)
B, E
224Klebsiella oxytocaGene Names: pddB
EC: 4.2.1.28
Find proteins for Q59471 (Klebsiella oxytoca)
Go to UniProtKB:  Q59471
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DIOL DEHYDRATASE)
G, M
173Klebsiella oxytocaGene Names: pddC (pduE)
EC: 4.2.1.28
Find proteins for Q59472 (Klebsiella oxytoca)
Go to UniProtKB:  Q59472
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: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.200α = 90.00
b = 122.300β = 90.00
c = 209.600γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-30
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2012-10-24
    Type: Non-polymer description