PDBsum entry 1bwp

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protein links
Hydrolase PDB id
Protein chain
212 a.a. *
Waters ×145
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase
Structure: Platelet-activating factor acetylhydrolase. Chain: a. Synonym: pafah. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: brain. Tissue: brain. Cellular_location: cytoplasm. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Homo-Dimer (from PDB file)
2.10Å     R-factor:   0.209     R-free:   0.252
Authors: Y.S.Ho,P.J.Sheffield,J.Masuyama,H.Arai,J.Li,J.Aoki,K.Inoue, U.Derewenda,Z.Derewenda
Key ref: Y.S.Ho et al. (1999). Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase. Protein Eng, 12, 693-700. PubMed id: 10469831
27-Sep-98     Release date:   18-May-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q29460  (PA1B3_BOVIN) -  Platelet-activating factor acetylhydrolase IB subunit gamma
232 a.a.
212 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.  - 1-alkyl-2-acetylglycerophosphocholine esterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H2O = 1-alkyl- sn-glycero-3-phosphocholine + acetate
+ H(2)O
= 1-alkyl- sn-glycero-3-phosphocholine
+ acetate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     lipid metabolic process   3 terms 
  Biochemical function     hydrolase activity     2 terms  


    Added reference    
Protein Eng 12:693-700 (1999)
PubMed id: 10469831  
Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase.
Y.S.Ho, P.J.Sheffield, J.Masuyama, H.Arai, J.Li, J.Aoki, K.Inoue, U.Derewenda, Z.S.Derewenda.
Platelet-activating factor acetylhydrolases (PAF-AHs) are unique PLA2s which hydrolyze the sn-2 ester linkage in PAF-like phospholipids with a marked preference for very short acyl chains, typically acetyl. The recent solution of the crystal structure of the alpha(1) catalytic subunit of isoform Ib of bovine brain intracellular PAF-AH at 1.7 A resolution paved the way for a detailed examination of the molecular basis of substrate specificity in this enzyme. The crystal structure suggests that the side chains of Thr103, Leu48 and Leu194 are involved in substrate recognition. Three single site mutants (L48A, T103S and L194A) were overexpressed and their structures were solved to 2.3 A resolution or better by X-ray diffraction methods. Enzyme kinetics showed that, compared with wild-type protein, all three mutants have higher relative activity against phospholipids with sn-2 acyl chains longer than an acetyl. However, for each of the mutants we observed an unexpected and substantial reduction in the V(max) of the reaction. These results are consistent with the model in which residues Leu48, Thr103 and Leu194 indeed contribute to substrate specificity and in addition suggest that the integrity of the specificity pocket is critical for the expression of full catalytic function, thus conferring very high substrate selectivity on the enzyme.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20300652 D.E.Almonacid, E.R.Yera, J.B.Mitchell, and P.C.Babbitt (2010).
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.
  PLoS Comput Biol, 6, e1000700.  
  18838739 T.M.McIntyre, S.M.Prescott, and D.M.Stafforini (2009).
The emerging roles of PAF acetylhydrolase.
  J Lipid Res, 50, S255-S259.  
17957779 I.Martínez-Martínez, J.Navarro-Fernández, J.Daniel Lozada-Ramírez, F.García-Carmona, and A.Sánchez-Ferrer (2008).
YesT: a new rhamnogalacturonan acetyl esterase from Bacillus subtilis.
  Proteins, 71, 379-388.  
15802654 S.Quevillon-Cheruel, N.Leulliot, M.Graille, N.Hervouet, F.Coste, H.Bénédetti, C.Zelwer, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of yeast YHR049W/FSH1, a member of the serine hydrolase family.
  Protein Sci, 14, 1350-1356.
PDB code: 1ycd
14978301 C.Blouin, D.Butt, and A.J.Roger (2004).
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
  Protein Sci, 13, 608-616.  
15522763 C.C.Akoh, G.C.Lee, Y.C.Liaw, T.H.Huang, and J.F.Shaw (2004).
GDSL family of serine esterases/lipases.
  Prog Lipid Res, 43, 534-552.  
11294621 J.H.Min, C.Wilder, J.Aoki, H.Arai, K.Inoue, L.Paul, and M.H.Gelb (2001).
Platelet-activating factor acetylhydrolases: broad substrate specificity and lipoprotein binding does not modulate the catalytic properties of the plasma enzyme.
  Biochemistry, 40, 4539-4549.  
10801485 A.Mølgaard, S.Kauppinen, and S.Larsen (2000).
Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
  Structure, 8, 373-383.
PDB codes: 1deo 1dex
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