1MMF

Crystal structure of substrate free form of glycerol dehydratase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of substrate free form of glycerol dehydratase

Liao, D.I.Dotson, G.Turner, I.Reiss, L.Emptage, M.

(2003) J.Inorg.Biochem. 93: 84-91


  • PubMed Abstract: 
  • Glycerol dehydratase (GDH) and diol dehydratase (DDH) are highly homologous isofunctional enzymes that catalyze the elimination of water from glycerol and 1,2-propanediol (1,2-PD) to the corresponding aldehyde via a coenzyme B(12)-dependent radical m ...

    Glycerol dehydratase (GDH) and diol dehydratase (DDH) are highly homologous isofunctional enzymes that catalyze the elimination of water from glycerol and 1,2-propanediol (1,2-PD) to the corresponding aldehyde via a coenzyme B(12)-dependent radical mechanism. The crystal structure of substrate free form of GDH in complex with cobalamin and K(+) has been determined at 2.5 A resolution. Its overall fold and the subunit assembly closely resemble those of DDH. Comparison of this structure and the DDH structure, available only in substrate bound form, shows the expected change of the coordination of the essential K(+) from hexacoordinate to heptacoordinate with the displacement of a single coordinated water by the substrate diol. In addition, there appears to be an increase in the rigidity of the K(+) coordination (as measured by lower B values) upon the binding of the substrate. Structural analysis of the locations of conserved residues among various GDH and DDH sequences has aided in identification of residues potentially important for substrate preference or specificity of protein-protein interactions.


    Organizational Affiliation

    DuPont Central Research and Development, Experimental Station, Wilmington, DE 19880, USA. der-ing.liao@usa.dupont.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glycerol dehydrase 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 dehydrase 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 dehydrase 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 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.700α = 90.00
b = 110.070β = 107.64
c = 114.690γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-10-24
    Type: Non-polymer description