Crystal structure of F114R/R117A mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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Examining the Role of Intersubunit Contacts in Catalysis by 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase.

Allison, T.M.Cochrane, F.C.Jameson, G.B.Parker, E.J.

(2013) Biochemistry 52: 4676-4686

  • DOI: https://doi.org/10.1021/bi400521f
  • Primary Citation of Related Structures:  
    4JTE, 4JTF, 4JTG, 4JTH, 4JTI, 4JTJ, 4JTK, 4JTL

  • PubMed Abstract: 

    3-Deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) catalyzes the reaction between phosphoenolpyruvate and arabinose 5-phosphate (A5P) in the first committed step in the pathway to 3-deoxy-d-manno-octulosonate, a component in the cell wall of Gram-negative bacteria. KDO8PS is evolutionarily and structurally related to the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS), which uses erythrose 4-phosphate in place of A5P. Both KDO8PS and type Iβ DAH7PS enzymes adopt similar homotetrameric associations with their active sites close to one of the interfaces. The conserved PAFLxR motif in KDO8PS and the corresponding GARNxQ motif in type Iβ DAH7PS, both on the short β4-α4 loop of the (β/α)8 barrel, form part of this interface and provide key contacts with substrates. This (112)PAFLxR(117) motif was mutated in Neisseria meningitidis KDO8PS in order to assess its role in enzyme function. Arg117 extends across the interface to provide guanidinium functionality in the A5P binding site of the adjacent subunit. Substitution Arg117Ala severely hampered catalysis, whereas substitution to Lys was tolerated better. Mutation of Phe114 to either Arg or Ala results in active proteins, but with substantially elevated Km(A5P) values. Mutant proteins that combine substitutions in this motif demonstrate poor catalytic function, and, although these mutated residues now structurally resemble their counterparts in the GARNxQ motif of type Iβ DAH7PS, no DAH7PS-like activity was observed. Analysis of the structures reveals that small changes in relative orientation of the subunits are important for the differences in active-site construction. Quaternary structure is therefore tightly linked to substrate specificity.

  • Organizational Affiliation

    Institute of Fundamental Sciences, Massey University , Palmerston North, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase
A, B, C, D
280Neisseria meningitidis MC58Mutation(s): 2 
Gene Names: kdsANMB1283
Find proteins for Q9JZ55 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JZ55 
Go to UniProtKB:  Q9JZ55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JZ55
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth B]
G [auth C]
I [auth C]
J [auth D]
E [auth A],
F [auth B],
G [auth C],
I [auth C],
J [auth D],
K [auth D]
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.59α = 90
b = 85.37β = 90
c = 163.35γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2013-12-18
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description