PDBsum entry 1une

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Hydrolase PDB id
Protein chain
123 a.a. *
Waters ×134
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Carboxylic ester hydrolase, 1.5 angstrom orthorhombic form of the bovine recombinant pla2
Structure: Phospholipase a2. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Cell_line: bl21. Organ: pancreatic. Gene: mature pla2. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.50Å     R-factor:   0.184     R-free:   0.228
Authors: M.Sundaralingam
Key ref:
K.Sekar and M.Sundaralingam (1999). High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2. Acta Crystallogr D Biol Crystallogr, 55, 46-50. PubMed id: 10089393 DOI: 10.1107/S0907444998006568
05-Nov-97     Release date:   06-May-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00593  (PA21B_BOVIN) -  Phospholipase A2
145 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Phospholipase A(2).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate
+ H(2)O
= 1-acylglycerophosphocholine
+ carboxylate
      Cofactor: Calcium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     lipid metabolic process   5 terms 
  Biochemical function     hydrolase activity     5 terms  


DOI no: 10.1107/S0907444998006568 Acta Crystallogr D Biol Crystallogr 55:46-50 (1999)
PubMed id: 10089393  
High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2.
K.Sekar, M.Sundaralingam.
The X-ray structure of recombinant bovine pancreatic phospholipase A2 (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 A resolution. The crystal belongs to the space group P212121 with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 A similar to the native enzyme reported previously by Dijkstra et al. [J. Mol. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (Rfree = 22.8%) for 16 374 reflections between 10.0 and 1.5 A resolution. The surface-loop residues (60-70) are ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis. The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion. In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.
  Selected figure(s)  
Figure 2.
Figure 2 A stereoview of (a) the omit electron-density map showing the ordered surface-loop residues 60-70 in the present orthorhombic form, contoured at the 1.0 level, and (b) the water molecules (open circles) involved in hydrogen bonding with the polar atoms of the surface-loop residues produced using the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).
Figure 4.
Figure 4 A stereoview of the hydrogen-bonding (dashed lines) network connecting the active/catalytic site and the calcium coordination sphere. The omit electron-density map shows the five water molecules commonly found in the active site: the structural water (W11), the two calcium-coordinated waters (W5 and W12), the catalytic water (W6) and the second water (W7). Contours are shown at the 1.0 level.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 46-50) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
  16511247 K.Sekar, M.Yogavel, D.Gayathri, D.Velmurugan, R.Krishna, M.J.Poi, Z.Dauter, M.Dauter, and M.D.Tsai (2006).
Atomic resolution structure of the double mutant (K53,56M) of bovine pancreatic phospholipase A2.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1-5.  
  16508077 K.Sekar, V.Rajakannan, D.Gayathri, D.Velmurugan, M.J.Poi, M.Dauter, Z.Dauter, and M.D.Tsai (2005).
Atomic resolution (0.97 A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 3-7.
PDB codes: 1vl9 2bax
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