DB code: S00361

RLCP classification 1.12.30000.24 : Hydrolysis
CATH domain 3.40.50.1110 : Rossmann fold Catalytic domain
E.C. 3.1.1.47
CSA 1bwp
M-CSA 1bwp
MACiE M0094

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq
Q29460 Platelet-activating factor acetylhydrolase IB subunit gamma
EC 3.1.1.47
PAF acetylhydrolase 29 kDa subunit
PAF-AH 29 kDa subunit
PAF-AH subunit gamma
PAFAH subunit gamma
NP_777090.1 (Protein)
NM_174665.2 (DNA/RNA sequence)

KEGG enzyme name
1-alkyl-2-acetylglycerophosphocholine esterase
1-alkyl-2-acetyl-sn-glycero-3-phosphocholine acetylhydrolase
alkylacetyl-GPC:acetylhydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q29460 PA1B3_BOVIN 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H(2)O = 1-alkyl-sn-glycero-3-phosphocholine + acetate. Cytosolic 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. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00565 Ether lipid metabolism

Compound table
Substrates Products Intermediates
KEGG-id C04598 C00001 C04317 C00033
E.C.
Compound 1-Alkyl-2-acetyl-sn-glycero-3-phosphocholine H2O 1-Alkyl-sn-glycerol-3-phosphocholine Acetate
Type amine group,carbohydrate,lipid,phosphate group/phosphate ion H2O amine group,carbohydrate,lipid,phosphate group/phosphate ion carboxyl group
ChEBI 15377
15366
PubChem 22247451
962
176
21980959
1bwpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bwqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1bwrA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1es9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1wabA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ACT

Reference for Active-site residues
resource references E.C.
Swiss-prot;Q29460

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bwpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 47;ASN 104;ASP 192;HIS 195 SER 47;GLY 74
1bwqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 47;ASN 104;ASP 192;HIS 195 SER 47;GLY 74
1bwrA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 47;ASN 104;ASP 192;HIS 195 SER 47;GLY 74
1es9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 47;ASN 104;ASP 192;HIS 195 SER 47;GLY 74
1wabA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 47;ASN 104;ASP 192;HIS 195 SER 47;GLY 74

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.90-92.
[2]
p.698-699
[4]
p.869-870

References
[1]
Resource
Comments X-ray crystallography (1.7 Angstroms)
Medline ID
PubMed ID 8985254
Journal Nature
Year 1997
Volume 385
Pages 89-93
Authors Ho YS, Swenson L, Derewenda U, Serre L, Wei Y, Dauter Z, Hattori M, Adachi T, Aoki J, Arai H, Inoue K, Derewenda ZS
Title Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer.
Related PDB 1wab
Related UniProtKB
[2]
Resource
Comments X-ray crystallography (1.7 Angstroms)
Medline ID
PubMed ID 10469831
Journal Protein Eng
Year 1999
Volume 12
Pages 693-700
Authors Ho YS, Sheffield PJ, Masuyama J, Arai H, Li J, Aoki J, Inoue K, Derewenda U, Derewenda ZS
Title Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase.
Related PDB 1bwp 1bwq 1bwr
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 11080681
Journal Biochim Biophys Acta
Year 2000
Volume 1488
Pages 102-23
Authors Tjoelker LW, Stafforini DM
Title Platelet-activating factor acetylhydrolases in health and disease.
Related PDB
Related UniProtKB
[4]
Resource
Comments functional consequences of the dimerization
Medline ID
PubMed ID 11239086
Journal Protein Eng
Year 2000
Volume 13
Pages 865-71
Authors McMullen TW, Li J, Sheffield PJ, Aoki J, Martin TW, Arai H, Inoue K, Derewenda ZS
Title The functional implications of the dimerization of the catalytic subunits of the mammalian brain platelet-activating factor acetylhydrolase (Ib).
Related PDB 1es9
Related UniProtKB
[5]
Resource
Comments X-ray crystallography (2.1 Angstroms)
Medline ID
PubMed ID 11522926
Journal Protein Eng
Year 2001
Volume 14
Pages 513-9
Authors Sheffield PJ, McMullen TW, Li J, Ho YS, Garrard SM, Derewenda U, Derewenda ZS
Title Preparation and crystal structure of the recombinant alpha(1)/alpha(2) catalytic heterodimer of bovine brain platelet-activating factor acetylhydrolase Ib.
Related PDB
Related UniProtKB

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].

Created Updated
2002-07-04 2010-11-30