1EEX

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 

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Literature

How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.

Masuda, J.Shibata, N.Morimoto, Y.Toraya, T.Yasuoka, N.

(2000) Structure 8: 775-788

  • DOI: https://doi.org/10.1016/s0969-2126(00)00164-7
  • Primary Citation of Related Structures:  
    1EEX, 1EGM, 1EGV

  • PubMed Abstract: 

    Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for enzymatic radical reactions. The adenosyl radical, a catalytic radical in these reactions, is formed by homolysis of the cobalt-carbon bond of the coenzyme, although the mechanism of cleavage of its organometallic bond remains unsolved. We determined the three-dimensional structures of diol dehydratase complexed with adeninylpentylcobalamin and with cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic temperatures. In the adeninylpentylcobalamin complex, the adenine ring is bound parallel to the corrin ring as in the free form and methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing pyrrole ring C. All of its nitrogen atoms except for N(9) are hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a sidechain hydroxyl group, and a water molecule. As compared with the cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120 degrees to hydrogen bond with N(3) of the adenine ring. The structure of the adenine-ring-binding site provides a molecular basis for the strict specificity of diol dehydratase for the coenzyme adenosyl group. The superimposition of the structure of the free coenzyme on that of enzyme-bound adeninylpentylcobalamin demonstrated that the tight enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring of the adenosyl group would inevitably lead to cleavage of the cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic linkage makes the 5'-carbon radical accessible to the hydrogen atom of the substrate to be abstracted.


  • Organizational Affiliation

    Department of Life Science, Himeji Institute of Technology, Kamigori, Akogun, 678-1297, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASEA,
D [auth L]
554Klebsiella oxytocaMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASE
B, E
224Klebsiella oxytocaMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROPANEDIOL DEHYDRATASEC [auth G],
F [auth M]
173Klebsiella oxytocaMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COY
Query on COY

Download Ideal Coordinates CCD File 
I [auth A],
M [auth L]
CO-(ADENIN-9-YL-PENTYL)-COBALAMIN
C72 H106 Co N18 O14 P
KWGNLVVAVJCVFN-OGKXECBZSA-N
PGO
Query on PGO

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.38α = 90
b = 121.4β = 90
c = 207.6γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COYClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy, Structure summary