1DIO

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


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 7: 997-1008

  • DOI: 10.1016/s0969-2126(99)80126-9
  • Primary Citation of Related Structures:  
    1DIO

  • 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 radical mechanism ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DIOL DEHYDRATASE)A,
D [auth L]
554Klebsiella oxytocaMutation(s): 0 
Gene Names: pddA
EC: 4.2.1.28
UniProt
Find proteins for Q59470 (Klebsiella oxytoca)
Explore Q59470 
Go to UniProtKB:  Q59470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59470
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DIOL DEHYDRATASE)B, E224Klebsiella oxytocaMutation(s): 0 
Gene Names: pddB
EC: 4.2.1.28
UniProt
Find proteins for Q59471 (Klebsiella oxytoca)
Explore Q59471 
Go to UniProtKB:  Q59471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59471
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DIOL DEHYDRATASE)C [auth G],
F [auth M]
173Klebsiella oxytocaMutation(s): 0 
Gene Names: pddCDVB85_01585
EC: 4.2.1.28
UniProt
Find proteins for Q59472 (Klebsiella oxytoca)
Explore Q59472 
Go to UniProtKB:  Q59472
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59472
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download Ideal Coordinates CCD File 
I [auth B],
L [auth E]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
PGO
Query on PGO

Download Ideal Coordinates CCD File 
H [auth A],
K [auth L]
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A],
J [auth L]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.2α = 90
b = 122.3β = 90
c = 209.6γ = 90
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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