1V0Y | pdb_00001v0y

Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

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 Biology 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOLIPASE D506Streptomyces sp. PMFMutation(s): 0 
EC: 3.1.4.4
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HI5
Query on HI5

Download Ideal Coordinates CCD File 
B [auth A]2-(BUTYRYLOXY)-1-{[(TETRAHYDROXYPHOSPHORANYL)OXY]METHYL}ETHYL BUTYRATE
C11 H23 O9 P
YBSWGBVCGAZBHG-SECBINFHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.369α = 90
b = 56.462β = 93.74
c = 68.762γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HI5Click on this verticalbar to view details

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, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary