3AUJ

Structure of diol dehydratase complexed with glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols

Yamanishi, M.Kinoshita, K.Fukuoka, M.Saito, T.Tanokuchi, A.Ikeda, Y.Obayashi, H.Mori, K.Shibata, N.Tobimatsu, T.Toraya, T.

(2012) Febs J. 279: 793-804

  • DOI: 10.1111/j.1742-4658.2012.08470.x

  • PubMed Abstract: 
  • Coenzyme B(12) dependent diol dehydratase undergoes mechanism-based inactivation by glycerol, accompanying the irreversible cleavage of the coenzyme Co-C bond. Bachovchin et al. [Biochemistry16, 1082-1092 (1977)] reported that glycerol bound in the G ...

    Coenzyme B(12) dependent diol dehydratase undergoes mechanism-based inactivation by glycerol, accompanying the irreversible cleavage of the coenzyme Co-C bond. Bachovchin et al. [Biochemistry16, 1082-1092 (1977)] reported that glycerol bound in the G(S) conformation, in which the pro-S-CH(2) OH group is oriented to the hydrogen-abstracting site, primarily contributes to the inactivation reaction. To understand the mechanism of inactivation by glycerol, we analyzed the X-ray structure of diol dehydratase complexed with cyanocobalamin and glycerol. Glycerol is bound to the active site preferentially in the same conformation as that of (S)-1,2-propanediol, i.e. in the G(S) conformation, with its 3-OH group hydrogen bonded to Serα301, but not to nearby Glnα336. k(inact) of the Sα301A, Qα336A and Sα301A/Qα336A mutants with glycerol was much smaller than that of the wild-type enzyme. k(cat) /k(inact) showed that the Sα301A and Qα336A mutants are substantially more resistant to glycerol inactivation than the wild-type enzyme, suggesting that Serα301 and Glnα336 are directly or indirectly involved in the inactivation. The degree of preference for (S)-1,2-propanediol decreased on these mutations. The substrate activities towards longer chain 1,2-diols significantly increased on the Sα301A/Qα336A double mutation, probably because these amino acid substitutions yield more space for accommodating a longer alkyl group on C3 of 1,2-diols. Database Structural data are available in the Protein Data Bank under the accession number 3AUJ. Structured digital abstract • Diol dehydrase gamma subunit, Diol dehydrase beta subunit and Diol dehydrase alpha subunit physically interact by X-ray crystallography (View interaction).


    Organizational Affiliation

    Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diol dehydrase alpha subunit
A, L
554Klebsiella oxytocaMutation(s): 0 
Gene Names: pddA (pduC)
EC: 4.2.1.28
Find proteins for Q59470 (Klebsiella oxytoca)
Go to UniProtKB:  Q59470
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Diol dehydrase beta subunit
B, E
224Klebsiella oxytocaMutation(s): 0 
Gene Names: pddB (pduD)
EC: 4.2.1.28
Find proteins for Q59471 (Klebsiella oxytoca)
Go to UniProtKB:  Q59471
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Diol dehydrase gamma subunit
G, M
173Klebsiella oxytocaMutation(s): 0 
Gene Names: pddC (pduE)
EC: 4.2.1.28
Find proteins for Q59472 (Klebsiella oxytoca)
Go to UniProtKB:  Q59472
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, E, G, L, M
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 190.610α = 90.00
b = 196.800β = 95.03
c = 77.360γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
HKL-2000data scaling
BSSdata collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Non-polymer description
  • Version 1.2: 2013-06-19
    Type: Database references