EzCatDB: S00361

DB codeS00361
RLCP classification1.12.30000.24
CATH domainDomain 13.40.50.1110Catalytic domain
E.C.3.1.1.47
CSA1bwp
MACiEM0094


Enzyme Name
Swiss-protKEGG

Q29460
Protein namePlatelet-activating factor acetylhydrolase IB subunit gamma1-alkyl-2-acetylglycerophosphocholine esterase
1-alkyl-2-acetyl-sn-glycero-3-phosphocholine acetylhydrolase
alkylacetyl-GPC:acetylhydrolase
SynonymsEC 3.1.1.47
PAF acetylhydrolase 29 kDa subunit
PAF-AH 29 kDa subunit
PAF-AH subunit gamma
PAFAH subunit gamma

KEGG pathways
MAP codePathways
MAP00565Ether lipid metabolism

Swiss-prot:Accession NumberQ29460
Entry namePA1B3_BOVIN
Activity1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H(2)O = 1-alkyl-sn-glycero-3-phosphocholine + acetate.
SubunitCytosolic PAF-AH IB is formed of three subunits of 45 kDa (alpha), 30 kDa (beta) and 29 kDa (gamma). The catalytic activity of the enzyme resides in the beta and gamma subunits, whereas the alpha subunit has regulatory activity. Trimer formation is not essential for the catalytic activity.
Subcellular locationCytoplasm.
Cofactor


SubstratesProducts
KEGG-idC04598C00001C04317C00033
Compound1-Alkyl-2-acetyl-sn-glycero-3-phosphocholineH2O1-Alkyl-sn-glycerol-3-phosphocholineAcetate
Typeamine group,carbohydrate,lipid,phosphate group/phosphate ionH2Oamine group,carbohydrate,lipid,phosphate group/phosphate ioncarboxyl group
1bwpAUnbound
UnboundUnbound
1bwqAUnbound
UnboundUnbound
1bwrAUnbound
UnboundUnbound
1es9AUnbound
UnboundUnbound
1wabAUnbound
UnboundBound:ACT

Active-site residues
resource
Swiss-prot;Q29460
pdbCatalytic residuesMain-chain involved in catalysis
1bwpASER 47;ASN 104;ASP 192;HIS 195
SER 47;GLY 74
1bwqASER 47;ASN 104;ASP 192;HIS 195
SER 47;GLY 74
1bwrASER 47;ASN 104;ASP 192;HIS 195
SER 47;GLY 74
1es9ASER 47;ASN 104;ASP 192;HIS 195
SER 47;GLY 74
1wabASER 47;ASN 104;ASP 192;HIS 195
SER 47;GLY 74

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.90-92.
[2]p.698-699
[4]p.869-870

references
[1]
CommentsX-ray crystallography (1.7 Angstroms)
PubMed ID8985254
JournalNature
Year1997
Volume385
Pages89-93
AuthorsHo YS, Swenson L, Derewenda U, Serre L, Wei Y, Dauter Z, Hattori M, Adachi T, Aoki J, Arai H, Inoue K, Derewenda ZS
TitleBrain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer.
Related PDB1wab
[2]
CommentsX-ray crystallography (1.7 Angstroms)
PubMed ID10469831
JournalProtein Eng
Year1999
Volume12
Pages693-700
AuthorsHo YS, Sheffield PJ, Masuyama J, Arai H, Li J, Aoki J, Inoue K, Derewenda U, Derewenda ZS
TitleProbing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase.
Related PDB1bwp,1bwq,1bwr
[3]
PubMed ID11080681
JournalBiochim Biophys Acta
Year2000
Volume1488
Pages102-23
AuthorsTjoelker LW, Stafforini DM
TitlePlatelet-activating factor acetylhydrolases in health and disease.
[4]
Commentsfunctional consequences of the dimerization
PubMed ID11239086
JournalProtein Eng
Year2000
Volume13
Pages865-71
AuthorsMcMullen TW, Li J, Sheffield PJ, Aoki J, Martin TW, Arai H, Inoue K, Derewenda ZS
TitleThe functional implications of the dimerization of the catalytic subunits of the mammalian brain platelet-activating factor acetylhydrolase (Ib).
Related PDB1es9
[5]
CommentsX-ray crystallography (2.1 Angstroms)
PubMed ID11522926
JournalProtein Eng
Year2001
Volume14
Pages513-9
AuthorsSheffield PJ, McMullen TW, Li J, Ho YS, Garrard SM, Derewenda U, Derewenda ZS
TitlePreparation and crystal structure of the recombinant alpha(1)/alpha(2) catalytic heterodimer of bovine brain platelet-activating factor acetylhydrolase Ib.

comments
The paper [1] on the crystal structure of this enzyme reported that it has a trypsin-like catalytic triad of Ser47, His195 and Asp 192, as well as an oxyanion hole. Moreover, Ser47 has been identified as the putative nucleohile, whereas the oxyanion hole seems to be composed of mainchain amide groups of Ser47 and Gly74 along with sidechain amide of Asn104, according to this paper [1].
The paper [4] suggested that this enzyme has got another unique feature in the active site. Arg29 and Arg22 in one chain contribute to the catalytic site of the other monomer across the dimer interface. Thus, the dimerization is essential for both stability and catalytic activity of this enzyme [4].

createdupdated
2002-07-042010-11-30


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.