1DB3

E.COLI GDP-MANNOSE 4,6-DEHYDRATASE

• PDB DOI: https://doi.org/10.2210/pdb1DB3/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-11-02 Released: 1999-11-24 
• Deposition Author(s): Somoza, J.R., Menon, S., Somers, W.S., Sullivan, F.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose.

Somoza, J.R., Menon, S., Schmidt, H., Joseph-McCarthy, D., Dessen, A., Stahl, M.L., Somers, W.S., Sullivan, F.X.

(2000) Structure 8: 123-135

• PubMed: 10673432 
• DOI: https://doi.org/10.1016/s0969-2126(00)00088-5
• Primary Citation of Related Structures:  
  1DB3


• PubMed Abstract: 
  

  GDP-mannose 4,6 dehydratase (GMD) catalyzes the conversion of GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose. This is the first and regulatory step in the de novo biosynthesis of GDP-(L)-fucose. Fucose forms part of a number of glycoconjugates, including the ABO blood groups and the selectin ligand sialyl Lewis X. Defects in GDP-fucose metabolism have been linked to leukocyte adhesion deficiency type II (LADII).

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Organizational Affiliation: 

Wyeth Research, Cambridge, MA 02140, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.97 kDa 
• Atom Count: 2,754 
• Modelled Residue Count: 335 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-MANNOSE 4,6-DEHYDRATASE	A	372	Escherichia coli	Mutation(s): 0  EC: 4.2.1.47
UniProt
Find proteins for P0AC88 (Escherichia coli (strain K12)) Explore P0AC88  Go to UniProtKB:  P0AC88

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.6	α = 90
b = 149.6	β = 90
c = 102.6	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
ADSC	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-24 
Deposition Author(s): Somoza, J.R., Menon, S., Somers, W.S., Sullivan, F.X.

Revision History  

• Version 1.0: 1999-11-24
  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: 2024-02-07
  Changes: Data collection, Database references