PDBsum entry 1v0u

Hydrolase

PDB id: 1v0u

Contents

Protein chain

490 a.a. *

Ligands

PO3

Waters ×608

* Residue conservation analysis

PDB id:

1v0u

Name:

Hydrolase

Title:

Phospholipase d from streptomyces sp. Strain pmf soaked with the product glycerophosphate.

Structure:

Phospholipase d. Chain: a. Ec: 3.1.4.4

Source:

Streptomyces sp.. Organism_taxid: 172564. Strain: pmf

Resolution:

1.42Å R-factor: 0.167 R-free: 0.186

Authors:

I.Leiros,S.Mcsweeney,E.Hough

Key ref:

I.Leiros et al. (2004). 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, 805-820. PubMed id: 15165852 DOI: 10.1016/j.jmb.2004.04.003

Date:

02-Apr-04 Release date: 03-Jun-04

Protein chain

P84147  (P84147_STRSM) -  Phospholipase D from Streptomyces sp. (strain PMF)

Seq: 506 a.a.

Struc: 490 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.4.4 - phospholipase D.
• Reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1,2-diacyl-sn-glycero- 3-phosphate + choline + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.jmb.2004.04.003

J Mol Biol 339:805-820 (2004)

PubMed id: 15165852

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.

I.Leiros, S.McSweeney, E.Hough.

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.

Selected figure(s)

Figure 1.
Figure 1. The active site of PLD[PMF] unliganded or phosphate-inhibited. (a) The native state (structure 1). Two water molecules (OW1 and OW2) occupy the binding site for the phosphate moiety. (b) Phosphate-inhibited PLD[PMF] (structure 2). Both electron density maps are s[A]-weighted 2mF[o] -DF[c] maps contoured at 1.5s.

Figure 8.
Figure 8. The reaction mechanism for PLD[PMF] on a phosphatidylcholine (PC) substrate. R, Diacylglycerol (DAG); R', choline. The reaction that takes place when the product re-enters the active site and the dead-end phosphohistidine is formed is illustrated below the horizontal line.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 339, 805-820) copyright 2004.

Figures were selected by an automated process.