Crystal structure analysis of a mutant beta-ketoacyl-[acyl carrier protein] synthase II from Streptococcus pneumoniae

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.229 

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Roles of the active site water, histidine 303, and phenylalanine 396 in the catalytic mechanism of the elongation condensing enzyme of Streptococcus pneumoniae.

Zhang, Y.M.Hurlbert, J.White, S.W.Rock, C.O.

(2006) J Biol Chem 281: 17390-17399

  • DOI: https://doi.org/10.1074/jbc.M513199200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    beta-Ketoacyl-ACP synthases catalyze the condensation steps in fatty acid and polyketide synthesis and are targets for the development of novel antibiotics and anti-obesity and anti-cancer agents. The roles of the active site residues in Streptococcus pneumoniae FabF (beta-ketoacyl-ACP synthase II; SpFabF) were investigated to clarify the mechanism for this enzyme superfamily. The nucleophilic cysteine of the active site triad was required for acyl-enzyme formation and the overall condensation activity. The two active site histidines in the elongation condensing enzyme have different electronic states and functions. His337 is essential for condensation activity, and its protonated Nepsilon stabilizes the negative charge developed on the malonyl thioester carbonyl in the transition state. The Nepsilon of His303 accelerated catalysis by deprotonating a structured active site water for nucleophilic attack on the C3 of malonate, releasing bicarbonate. Lys332 controls the electronic state of His303 and also plays a critical role in the positioning of His337. Phe396 functions as a gatekeeper that controls the order of substrate addition. These data assign specific roles for each active site residue and lead to a revised general mechanism for this important class of enzymes.

  • Organizational Affiliation

    Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105. Electronic address: charles.rock@stjude.org.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxoacyl-(acyl-carrier-protein) synthase II431Streptococcus pneumoniaeMutation(s): 2 
Gene Names: 
EC: (PDB Primary Data), (UniProt)
Find proteins for Q9FBC2 (Streptococcus pneumoniae)
Explore Q9FBC2 
Go to UniProtKB:  Q9FBC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FBC2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.393α = 90
b = 88.82β = 90
c = 61.048γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description