Crystal structure of 2-Keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase from Pseudomonas aeruginosa.

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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Structure of 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase from Pseudomonas aeruginosa.

Nelson, S.K.Kelleher, A.Robinson, G.Reiling, S.Asojo, O.A.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1084-1088

  • DOI: https://doi.org/10.1107/S1744309113023993
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Pseudomonas aeruginosa is a major cause of opportunistic infection and is resistant to most antibiotics. As part of efforts to generate much-needed new antibiotics, structural studies of enzymes that are critical for the virulence of P. aeruginosa but are absent in mammals have been initiated. 2-Keto-3-deoxy-D-manno-octulosonate-8-phosphate synthase (KDO8Ps), also known as 2-dehydro-3-deoxyphosphooctonate aldolase, is vital for the survival and virulence of P. aeruginosa. This enzyme catalyzes a key step in the synthesis of the lipopolysaccharide (LPS) of most Gram-negative bacteria: the condensation reaction between phosphoenolpyruvate (PEP) and arabinose 5-phosphate to produce 2-keto-3-deoxy-D-manno-octulosonate-8-phosphate (KDO8P). This step is vital for the proper synthesis and assembly of LPS and the survival of P. aeruginosa. Here, the recombinant expression, purification and crystal structure of KDO8Ps from P. aeruginosa are presented. Orthorhombic crystals were obtained by vapor diffusion in sitting drops in the presence of 1 mM phosphoenlpyruvate. The structure reveals the prototypical α/β TIM-barrel structure expected from this family of enzymes and contains a tetramer in the asymmetric unit.

  • Organizational Affiliation

    National School of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX 77030, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase
A, B, C, D
287Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: kdsAPA3636
Find proteins for Q9ZFK4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9ZFK4 
Go to UniProtKB:  Q9ZFK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZFK4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.27α = 90
b = 95.1β = 90
c = 145.13γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2013-10-09 
  • Deposition Author(s): Asojo, O.A.

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2014-01-01
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description