1V0V

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

Summary for 1V0V

• Entry DOI: 10.2210/pdb1v0v/pdb
• Related: 1V0R 1V0S 1V0T 1V0U 1V0W 1V0Y
• Descriptor: PHOSPHOLIPASE D, PHOSPHITE ION (3 entities in total)
• Functional Keywords: phospholipase d, hydrolase, substrate soak, dibutyrylphosphatidylcholine, dic4pc
• Biological source: STREPTOMYCES SP.
• Total number of polymer chains: 1
• Total formula weight: 54143.43

Authors

Leiros, I.,McSweeney, S.,Hough, E. (deposition date: 2004-04-02, release date: 2004-06-03, Last modification date: 2023-12-13)

Primary citation

Leiros, I.,Mcsweeney, S.,Hough, E.
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
J.Mol.Biol., 339:805-, 2004

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.

PubMed: 15165852
DOI: 10.1016/J.JMB.2004.04.003

Experimental method

X-RAY DIFFRACTION (1.7 Å)