Uninhibited form of Phospholipase D from Streptomyces sp. strain PMF

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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The Reaction Mechanism of Phospholipase D from Streptomyces Sp. Strain Pmf. Snapshots Along the Reaction Pathway Reveal a Pentacoordinate Reaction Intermediate and an Unexpected Final Product

Leiros, I.Mcsweeney, S.Hough, E.

(2004) J Mol Biol 339: 805

  • DOI: https://doi.org/10.1016/j.jmb.2004.04.003
  • Primary Citation of Related Structures:  
    1V0R, 1V0S, 1V0T, 1V0U, 1V0V, 1V0W, 1V0Y

  • PubMed Abstract: 

    Almost all enzyme-catalysed phosphohydrolytic or phosphoryl transfer reactions proceed through a five-coordinated phosphorus transition state. This is also true for the phospholipase D superfamily of enzymes, where the active site usually is made up of two identical sequence repeats of an HKD motif, positioned around an approximate 2-fold axis, where the histidine and lysine residues are essential for catalysis. An almost complete reaction pathway has been elucidated by a series of experiments where crystals of phospholipase D from Streptomyces sp. strain PMF (PLD(PMF)) were soaked for different times with (i) a soluble poor, short-chained phospholipid substrate and (ii) with a product. The various crystal structures were determined to a resolution of 1.35-1.75 A for the different time-steps. Both substrate and product-structures were determined in order to identify the different reaction states and to examine if the reaction actually terminated on formation of phosphatidic acid (the true product of phospholipase D action) or could proceed even further. The results presented support the theory that the phospholipase D superfamily shares a common reaction mechanism, although different family members have very different substrate preferences and perform different catalytic reactions. Results also show that the reaction proceeds via a phosphohistidine intermediate and provide unambiguous identification of a catalytic water molecule, ideally positioned for apical attack on the phosphorus and consistent with an associative in-line phosphoryl transfer reaction. In one of the experiments an apparent five-coordinate phosphorus transition state is observed.

  • Organizational Affiliation

    Department of Chemistry, Faculty of Science, University of Tromsø, Tromsø, Norway. ingar.leiros@esrf.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOLIPASE D506Streptomyces sp. PMFMutation(s): 0 
Find proteins for P84147 (Streptomyces sp. (strain PMF))
Explore P84147 
Go to UniProtKB:  P84147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84147
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.41α = 90
b = 57.37β = 93.45
c = 68.62γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description