PDBsum entry 1kvx

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Hydrolase PDB id
Protein chain
123 a.a. *
Waters ×98
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Carboxylic ester hydrolase, single mutant d99a of bovine pancreatic pla2, 1.9 a orthorhombic form
Structure: Phospholipase a2. Chain: a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Cell_line: bl21. Organ: pancreas. Gene: mature pla2. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.90Å     R-factor:   0.200     R-free:   0.313
Authors: M.Sundaralingam
Key ref:
K.Sekar et al. (1999). Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2. Acta Crystallogr D Biol Crystallogr, 55, 443-447. PubMed id: 10089353 DOI: 10.1107/S0907444998013699
28-Apr-98     Release date:   18-Nov-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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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/S0907444998013699 Acta Crystallogr D Biol Crystallogr 55:443-447 (1999)
PubMed id: 10089353  
Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2.
K.Sekar, R.Biswas, Y.Li, M.Tsai, M.Sundaralingam.
Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 A resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3121. The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.
  Selected figure(s)  
Figure 3.
Figure 3 The same stereoview of the calcium coordination in (a) the mutant D49E and (b) in the trigonal recombinant PLA2 (Sekar et al., 1998[Sekar, K., Sekharudu, Y. C., Tsai, M.-D. & Sundaralingam, M. (1998). Acta Cryst. D54, 342-346.]). The calcium ion is shown as a solid circle. The equatorial calcium water W5 and the axial calcium water W12 are missing in the mutant and are shown as open circles. In the mutant, only one of the carboxylate O atoms is liganded to calcium, compared with the recombinant enzyme where Asp49 forms a bidentate ligation. Thus, calcium has only four ligands in the mutant while it has seven ligands in the recombinant enzyme.
Figure 4.
Figure 4 The omit electron density of the mutated residue Glu49 and the calcium ion. Contours are shown at the 1.0 level. Note that there are only four ligands around the calcium ion.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 443-447) copyright 1999.  
  Figures were selected by an automated process.  

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

  PubMed id Reference
17093191 J.O.Kim, B.K.Chakrabarti, A.Guha-Niyogi, M.K.Louder, J.R.Mascola, L.Ganesh, and G.J.Nabel (2007).
Lysis of human immunodeficiency virus type 1 by a specific secreted human phospholipase A2.
  J Virol, 81, 1444-1450.  
16669624 M.Rouault, L.D.Rash, P.Escoubas, E.Boilard, J.Bollinger, B.Lomonte, T.Maurin, C.Guillaume, S.Canaan, C.Deregnaucourt, J.Schrével, A.Doglio, J.M.Gutiérrez, M.Lazdunski, M.H.Gelb, and G.Lambeau (2006).
Neurotoxicity and other pharmacological activities of the snake venom phospholipase A2 OS2: the N-terminal region is more important than enzymatic activity.
  Biochemistry, 45, 5800-5816.  
  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
10449366 M.H.Gelb, W.Cho, and D.C.Wilton (1999).
Interfacial binding of secreted phospholipases A(2): more than electrostatics and a major role for tryptophan.
  Curr Opin Struct Biol, 9, 428-432.  
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