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PDBsum entry 1u4y

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protein ligands links
Hydrolase PDB id
1u4y
Jmol
Contents
Protein chain
496 a.a.
Ligands
PX6
Theoretical model
PDB id:
1u4y
Name: Hydrolase
Title: Ligand px6 docked to phospholipase d (1f0i)
Structure: Phospholipase d (1f0i). Chain: a. Ec: 3.1.4.4
Source: Streptomyces sp.. Bacteria. Strain: pmf
Authors: C.L.Aikens,A.T.Laederach,P.J.Reilly
Key ref:
C.L.Aikens et al. (2004). Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking. Proteins, 57, 27-35. PubMed id: 15326592 DOI: 10.1002/prot.20180
Date:
26-Jul-04     Release date:   05-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 496 a.a.
Key:    Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.3.1.4.4  - Phospholipase D.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphatidylcholine + H2O = choline + a phosphatidate
phosphatidylcholine
+ H(2)O
= choline
+ phosphatidate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1002/prot.20180 Proteins 57:27-35 (2004)
PubMed id: 15326592  
 
 
Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking.
C.L.Aikens, A.Laederach, P.J.Reilly.
 
  ABSTRACT  
 
The automated docking program AutoDock was used to dock nine phosphatidic acids (PAs), six phosphatidylcholines, five phosphatidylethanolamines, four phosphatidylglycerols, one phosphatidylinositol and two phosphatidylserines, which have two identical saturated fatty acid residues with an even numbers of carbon atoms, onto the active site of Streptomyces sp. PMF phospholipase D (PLD). Two PAs with one double bond on the fatty acid chain linked to the C2 of the glycerol residue were also docked. In general, binding energies become progressively more negative as fatty acid residues become longer. When these residues are of sufficient length, one is coiled against a hydrophobic cliff in a well that also holds the glycerol and phosphate residues and the head group, while the other generally is bound by a hydrophobic surface outside the well. Phosphatidylcholines have the only head group that is firmly bound by the active site, giving a possible structural explanation for the low selectivity of Streptomyces PLD for other phospholipid substrates.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Reactions catalyzed by PLD.
Figure 5.
Figure 5. Space-filling illustrations of the docking of (a) PA-14 and PA-14:1 and (b) PA-18 and PA-18:1 in the PLD active site. Hydrophobic (white), negatively-charged (red), and positively-charged (blue) surfaces. The positive surface at the center of the illustrations is composed of the putative catalytic residues His165 and His438, as well as Lys167 and Lys440. The hydrophobic cliff is at the bottom of the illustrations.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 57, 27-35) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
17459102 Y.Uesugi, J.Arima, M.Iwabuchi, and T.Hatanaka (2007).
Sensor of phospholipids in Streptomyces phospholipase D.
  FEBS J, 274, 2672-2681.  
16001418 C.Mulakala, and P.J.Reilly (2005).
Hypocrea jecorina (Trichoderma reesei) Cel7A as a molecular machine: A docking study.
  Proteins, 60, 598-605.  
16138313 C.Mulakala, and P.J.Reilly (2005).
Force calculations in automated docking: enzyme-substrate interactions in Fusarium oxysporum Cel7B.
  Proteins, 61, 590-596.  
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.  
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.