3B8X

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) H188N mutant with bound GDP-perosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

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This is version 1.1 of the entry. See complete history


Literature

GDP-4-Keto-6-deoxy-D-mannose 3-Dehydratase, Accommodating a Sugar Substrate in the Active Site.

Cook, P.D.Holden, H.M.

(2008) J Biol Chem 283: 4295-4303

  • DOI: 10.1074/jbc.M708893200
  • Primary Citation of Related Structures:  
    3B8X

  • PubMed Abstract: 
  • Colitose is a dideoxysugar found in the O-antigen of the lipopolysaccharide that coats the outer membrane of some Gram-negative bacteria. Four enzymes are required for its production starting from D-mannose-1-phosphate and GTP. The focus of this investigation is GDP-4-keto-6-deoxy-D-mannose 3-dehydratase or ColD, which catalyzes the removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxymannose ...

    Colitose is a dideoxysugar found in the O-antigen of the lipopolysaccharide that coats the outer membrane of some Gram-negative bacteria. Four enzymes are required for its production starting from D-mannose-1-phosphate and GTP. The focus of this investigation is GDP-4-keto-6-deoxy-D-mannose 3-dehydratase or ColD, which catalyzes the removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxymannose. The enzyme is pyridoxal 5'-phosphate-dependent, but unlike most of these proteins, the conserved lysine residue that covalently holds the cofactor in the active site is replaced with a histidine residue. Here we describe the three-dimensional structure of ColD, determined to 1.7A resolution, whereby the active site histidine has been replaced with an asparagine residue. For this investigation, crystals of the site-directed mutant protein were grown in the presence of GDP-4-amino-4,6-dideoxy-D-mannose (GDP-perosamine). The electron density map clearly reveals the presence of the sugar analog trapped in the active site as an external aldimine. The active site is positioned between the two subunits of the dimer. Whereas the pyrophosphoryl groups of the ligand are anchored to the protein via Arg-219 and Arg-331, the hydroxyl groups of the hexose only lie within hydrogen bonding distance to ordered water molecules. Interestingly, the hexose moiety of the ligand adopts a boat rather than the typically observed chair conformation. Activity assays demonstrate that this mutant protein cannot catalyze the dehydration step. Additionally, we report data revealing that wild-type ColD is able to catalyze the production of GDP-4-keto-3,6-dideoxymannose using GDP-perosamine instead of GDP-4-keto-6-deoxymannose as a substrate.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706-1544, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyridoxamine 5-phosphate-dependent dehydraseA, B390Escherichia coli O55:H7Mutation(s): 1 
Gene Names: wbdK
EC: 2.6.1
Find proteins for Q9F118 (Escherichia coli)
Explore Q9F118 
Go to UniProtKB:  Q9F118
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4M
Query on G4M

Download Ideal Coordinates CCD File 
G [auth A], O [auth B][(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate
C24 H36 N7 O19 P3
BNJJFFPICXKOFM-VMLLIFSYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.411α = 90
b = 98.123β = 90
c = 119.94γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
EPMRphasing
TNTrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance