PDBsum entry 1v0y

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Hydrolase PDB id
Protein chain
493 a.a. *
Waters ×413
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Phospholipase d from streptomyces sp. Strain pmf soaked with the substrate dibutyrylphosphatidylcholine.
Structure: Phospholipase d. Chain: a. Ec:
Source: Streptomyces sp.. Organism_taxid: 172564. Strain: pmf
1.71Å     R-factor:   0.162     R-free:   0.202
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
02-Apr-04     Release date:   03-Jun-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P84147  (P84147_STRSM) -  Phospholipase D
506 a.a.
493 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Phospholipase D.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphatidylcholine + H2O = choline + a phosphatidate
+ H(2)O
= choline
Bound ligand (Het Group name = HI5)
matches with 63.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20047964 G.Sasnauskas, L.Zakrys, M.Zaremba, R.Cosstick, J.W.Gaynor, S.E.Halford, and V.Siksnys (2010).
A novel mechanism for the scission of double-stranded DNA: BfiI cuts both 3'-5' and 5'-3' strands by rotating a single active site.
  Nucleic Acids Res, 38, 2399-2410.  
20077536 G.Yang, Y.Xu, J.Hou, H.Zhang, and Y.Zhao (2010).
Determination of the absolute configuration of pentacoordinate chiral phosphorus compounds in solution by using vibrational circular dichroism spectroscopy and density functional theory.
  Chemistry, 16, 2518-2527.  
20571626 G.Yang, Y.Xu, J.Hou, H.Zhang, and Y.Zhao (2010).
Diastereomers of the pentacoordinate chiral phosphorus compounds in solution: absolute configurations and predominant conformations.
  Dalton Trans, 39, 6953-6959.  
19241409 C.Morasso, T.Bellini, D.Monti, M.Bassi, D.Prosperi, and S.Riva (2009).
Dispersed phantom scatterer technique reveals subtle differences in substrate recognition by phospholipase D inactive mutants.
  Chembiochem, 10, 639-644.  
18338352 A.Masayama, T.Takahashi, K.Tsukada, S.Nishikawa, R.Takahashi, M.Adachi, K.Koga, A.Suzuki, T.Yamane, H.Nakano, and Y.Iwasaki (2008).
Streptomyces phospholipase D mutants with altered substrate specificity capable of phosphatidylinositol synthesis.
  Chembiochem, 9, 974-981.  
18824174 E.J.Drake, and A.M.Gulick (2008).
Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin.
  J Mol Biol, 384, 193-205.
PDB codes: 3e59 3eat
18398008 Z.Lu, D.Dunaway-Mariano, and K.N.Allen (2008).
The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state.
  Proc Natl Acad Sci U S A, 105, 5687-5692.
PDB codes: 2rar 2rav 2rb5 2rbk
17855396 S.H.Chan, Y.Bao, E.Ciszak, S.Laget, and S.Y.Xu (2007).
Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.
  Nucleic Acids Res, 35, 6238-6248.  
17451436 S.Stumpe, S.König, and R.Ulbrich-Hofmann (2007).
Insights into the structure of plant alpha-type phospholipase D.
  FEBS J, 274, 2630-2640.  
17189478 Y.Uesugi, J.Arima, M.Iwabuchi, and T.Hatanaka (2007).
C-terminal loop of Streptomyces phospholipase D has multiple functional roles.
  Protein Sci, 16, 197-207.  
17459102 Y.Uesugi, J.Arima, M.Iwabuchi, and T.Hatanaka (2007).
Sensor of phospholipids in Streptomyces phospholipase D.
  FEBS J, 274, 2672-2681.  
16433548 J.G.Zalatan, and D.Herschlag (2006).
Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis.
  J Am Chem Soc, 128, 1293-1303.  
16339153 L.G.Henage, J.H.Exton, and H.A.Brown (2006).
Kinetic analysis of a mammalian phospholipase D: allosteric modulation by monomeric GTPases, protein kinase C, and polyphosphoinositides.
  J Biol Chem, 281, 3408-3417.  
16129597 D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.
  Curr Opin Struct Biol, 15, 538-547.  
16150810 I.A.Cymerman, G.Meiss, and J.M.Bujnicki (2005).
DNase II is a member of the phospholipase D superfamily.
  Bioinformatics, 21, 3959-3962.  
15654080 M.T.Murakami, M.F.Fernandes-Pedrosa, D.V.Tambourgi, and R.K.Arni (2005).
Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D.
  J Biol Chem, 280, 13658-13664.
PDB codes: 1xx1 2f9r
15973486 R.Ulbrich-Hofmann, A.Lerchner, M.Oblozinsky, and L.Bezakova (2005).
Phospholipase D and its application in biocatalysis.
  Biotechnol Lett, 27, 535-544.  
15899903 Y.Uesugi, K.Mori, J.Arima, M.Iwabuchi, and T.Hatanaka (2005).
Recognition of phospholipids in Streptomyces phospholipase D.
  J Biol Chem, 280, 26143-26151.  
15691025 R.Sato, Y.Itabashi, A.Suzuki, T.Hatanaka, and A.Kuksis (2004).
Effect of temperature on the stereoselectivity of phospholipase D toward glycerol in the transphosphatidylation of phosphatidylcholine to phosphatidylglycerol.
  Lipids, 39, 1019-1023.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.