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Hydrolase PDB id
1g4i
Jmol
Contents
Protein chain
123 a.a. *
Ligands
MRD-MRD
MRD
MPD ×2
Metals
_CA
_CL
Waters ×266
* Residue conservation analysis
PDB id:
1g4i
Name: Hydrolase
Title: Crystal structure of the bovine pancreatic phospholipase a2
Structure: Phospholipase a2. Chain: a. Ec: 3.1.1.4
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
0.97Å     R-factor:   0.094    
Authors: R.A.Steiner,H.J.Rozeboom,A.De Vries,K.H.Kalk,G.N.Murshudov, K.S.Wilson,B.W.Dijkstra
Key ref:
R.A.Steiner et al. (2001). X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution. Acta Crystallogr D Biol Crystallogr, 57, 516-526. PubMed id: 11264580 DOI: 10.1107/S0907444901002530
Date:
27-Oct-00     Release date:   04-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.4  - Phospholipase A(2).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate
Phosphatidylcholine
 + 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   2 terms 
  Biological process     metabolic process   7 terms 
  Biochemical function     hydrolase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444901002530 Acta Crystallogr D Biol Crystallogr 57:516-526 (2001)
PubMed id: 11264580  
 
 
X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution.
R.A.Steiner, H.J.Rozeboom, A.de Vries, K.H.Kalk, G.N.Murshudov, K.S.Wilson, B.W.Dijkstra.
 
  ABSTRACT  
 
Using synchrotron radiation and a CCD camera, X-ray data have been collected from wild-type bovine pancreatic phospholipase A(2) at 100 K to 0.97 A resolution allowing full anisotropic refinement. The final model has a conventional R factor of 9.44% for all reflections, with a mean standard uncertainty for the positional parameters of 0.031 A as calculated from inversion of the full positional least-squares matrix. At 0.97 A resolution, bovine pancreatic phospholipase A(2) reveals for the first time that its rigid scaffolding does not preclude flexibility, which probably plays an important role in the catalytic process. Functionally important regions (the interfacial binding site and calcium-binding loop) are located at the molecular surface, where conformational variability is more pronounced. A cluster of 2-methyl-2,4-pentanediol molecules is present at the entrance of the hydrophobic channel that leads to the catalytic site and mimics the fatty-acid chains of a substrate analogue. Bovine pancreatic phospholipase A(2) at atomic resolution is compared with previous crystallographic structures and with models derived from nuclear magnetic resonance studies. Given the high structural similarity among extracellular phospholipases A(2) observed so far at lower resolution, the results arising from this structural analysis are expected to be of general validity for this class of enzymes.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Schematic drawing of the structure of bovine pancreatic phospholipase A[2] viewed in the direction of the plane of the interfacial activation site. The central hole loosely corresponds to the hydrophobic channel leading to the catalytic site. Strands are shown as arrows and helices as spirals. -helices are labelled A, B, C, D and E; 3[10]-helices are labelled I, II and III; N and C represent the N-terminus and C-terminus. The seven disulfide bridges are also shown. Colouring is according to B[eq]: colour ramping is from orange (lower B[eq]) to green (higher B[eq]). The essential calcium ion is depicted as an ochre sphere. This figure was generated with the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. (1991). J. Appl. Cryst. 24, 946-950.]). 		Figure 5.
Figure 5 Side and top views of the interfacial recognition site (IRS). Residues proposed by Dijkstra, Drenth et al. (1981[Dijkstra, B. W., Drenth, J. & Kalk, K. H. (1981). Nature (London), 289, 604-606.]) to constitute the IRS are shown. Most of them are seen in double conformations (major in green, minor in pink) at AR. IRS residues in single conformation (brown) are located in the most flexible regions of the protein [surface 3[10]-helix (67-72) and C-terminus]. In light and dark red newly proposed IRS residues (Lys10, Glu92 and Lys120) are shown. The essential calcium ion is shown as an ochre sphere. The MPD cluster (three MPD molecules with occupancies of 0.54, 0.51 and 0.26) seen near the calcium ion is displayed in yellow. This figure was generated with the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. (1991). J. Appl. Cryst. 24, 946-950.]).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 516-526) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19297324 W.Xu, L.Yi, Y.Feng, L.Chen, and J.Liu (2009).
Structural insight into the activation mechanism of human pancreatic prophospholipase A2.
  J Biol Chem, 284, 16659-16666.
PDB code: 3elo
18275084 D.P.Marchi-Salvador, L.C.Corrêa, A.J.Magro, C.Z.Oliveira, A.M.Soares, and M.R.Fontes (2008).
Insights into the role of oligomeric state on the biological activities of crotoxin: crystal structure of a tetrameric phospholipase A2 formed by two isoforms of crotoxin B from Crotalus durissus terrificus venom.
  Proteins, 72, 883-891.
PDB code: 2qog
17434532 Y.H.Pan, and B.J.Bahnson (2007).
Structural basis for bile salt inhibition of pancreatic phospholipase A2.
  J Mol Biol, 369, 439-450.
PDB codes: 2azy 2azz 2b00 2b01 2b03 2b04
  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
15304506 M.J.Nagiec, B.Lei, S.K.Parker, M.L.Vasil, M.Matsumoto, R.M.Ireland, S.B.Beres, N.P.Hoe, and J.M.Musser (2004).
Analysis of a novel prophage-encoded group A Streptococcus extracellular phospholipase A(2).
  J Biol Chem, 279, 45909-45918.  
12444963 P.Prijatelj, I.Krizaj, B.Kralj, F.Gubensek, and J.Pungercar (2002).
The C-terminal region of ammodytoxins is important but not sufficient for neurotoxicity.
  Eur J Biochem, 269, 5759-5764.  
12161451 Y.H.Pan, B.Z.Yu, A.G.Singer, F.Ghomashchi, G.Lambeau, M.H.Gelb, M.K.Jain, and B.J.Bahnson (2002).
Crystal structure of human group X secreted phospholipase A2. Electrostatically neutral interfacial surface targets zwitterionic membranes.
  J Biol Chem, 277, 29086-29093.
PDB codes: 1le6 1le7
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 code is shown on the right.