1MMF

Crystal structure of substrate free form of glycerol dehydratase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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

  • DOI: https://doi.org/10.1016/s0162-0134(02)00523-8
  • Primary Citation of Related Structures:  
    1MMF

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glycerol dehydrase alpha subunitA,
D [auth L]
555Klebsiella pneumoniaeMutation(s): 0 
EC: 4.2.1.30
UniProt
Find proteins for Q59476 (Klebsiella pneumoniae)
Explore Q59476 
Go to UniProtKB:  Q59476
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59476
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
glycerol dehydrase beta subunit
B, E
194Klebsiella pneumoniaeMutation(s): 0 
EC: 4.2.1.30 (PDB Primary Data), 4.2.1.28 (UniProt)
UniProt
Find proteins for O08505 (Klebsiella pneumoniae)
Explore O08505 
Go to UniProtKB:  O08505
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08505
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
glycerol dehydrase gamma subunitC [auth G],
F [auth M]
141Klebsiella pneumoniaeMutation(s): 0 
EC: 4.2.1.30 (PDB Primary Data), 4.2.1.28 (UniProt)
UniProt
Find proteins for Q59475 (Klebsiella pneumoniae)
Explore Q59475 
Go to UniProtKB:  Q59475
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59475
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.7α = 90
b = 110.07β = 107.64
c = 114.69γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-10-24
    Changes: Non-polymer description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description