EzCatDB: S00127

DB codeS00127
RLCP classification1.12.38700.511
CATH domainDomain 12.40.230.10Catalytic domain
E.C.3.1.1.4,3.1.1.32
CSA1qd6


Enzyme Name
Swiss-protKEGG

P0A921
Protein namePhospholipase A1phospholipase A2
   (EC 3.1.1.4)
lecithinase A
   (EC 3.1.1.4)
phosphatidase
   (EC 3.1.1.4)
phosphatidolipase
   (EC 3.1.1.4)
phospholipase A
   (EC 3.1.1.4)
phospholipase A1
   (EC 3.1.1.32)
SynonymsEC 3.1.1.32
EC 3.1.1.4
Detergent-resistant phospholipase A
DR-phospholipase A
Phosphatidylcholine 1-acylhydrolase
Outer membrane phospholipase A
OM PLA
OMPLA

KEGG pathways
MAP codePathwaysE.C.
MAP00564Glycerophospholipid metabolism3.1.1.4,3.1.1.32
MAP00565Ether lipid metabolism3.1.1.4
MAP00590Arachidonic acid metabolism3.1.1.4
MAP00591Linoleic acid metabolism3.1.1.4
MAP00592alpha-Linolenic acid metabolism3.1.1.4,3.1.1.32

Swiss-prot:Accession NumberP0A921
Entry namePA1_ECOLI
ActivityPhosphatidylcholine + H(2)O = 2-acylglycerophosphocholine + a carboxylate.,Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate.
SubunitHomodimer.
Subcellular locationCell outer membrane. Note=One of the very few enzymes located there.
CofactorCalcium.


CofactorsSubstratesProductsintermediates
KEGG-idC00076C00157C00001C04230C04233C00060I00123I00085I00086
E.C.
3.1.1.4,3.1.1.323.1.1.4,3.1.1.323.1.1.43.1.1.323.1.1.4,3.1.1.323.1.1.4,3.1.1.323.1.1.4,3.1.1.323.1.1.4,3.1.1.32
CompoundCalciumPhosphatidylcholineH2O1-Acyl-sn-glycero-3-phosphocholine2-Acyl-sn-glycero-3-phosphocholineCarboxylatePeptidyl-Ser-tetrahedral intermediate (with previous carboxylic-ester)Acyl-enzyme(Peptidyl-Ser-acyl group)Peptidyl-Ser-tetrahedral-intermediate
Typedivalent metal (Ca2+, Mg2+)amine group,carbohydrate,lipid,phosphate group/phosphate ionH2Oamine group,carbohydrate,lipid,phosphate group/phosphate ionamine group,carbohydrate,lipid,phosphate group/phosphate ioncarboxyl group


1fw2AUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1fw3AUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1fw3BUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1ildAUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1ilzAUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1im0AUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1qd5AUnboundUnbound
UnboundUnboundUnboundUnboundUnboundUnbound
1qd6CBound:_CAUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:HDS
1qd6DBound:_CAUnbound
UnboundUnboundUnboundUnboundUnboundTransition-state-analogue:HDS

Active-site residues
resource
Swiss-prot;P0A921 & literature [6], [7] & [11]
pdbCatalytic residuesCofactor-binding residuesModified residuesMain-chain involved in catalysiscomment
1fw2AHIS 142;SER 144;ASN 156
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
                     
GLY 146

1fw3AHIS 142;       ;ASN 156
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
S1H 144(sulfonylated)
GLY 146

1fw3BHIS 142;       ;ASN 156
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
S1H 144(sulfonylated)
GLY 146

1ildAHIS 142;SER 144;       
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
                     
GLY 146
mutant N156A
1ilzAHIS 142;SER 144;       
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
                     
GLY 146
mutant N156A
1im0AHIS 142;SER 144;       
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
                     
GLY 146
mutant N156A
1qd5AHIS 142;SER 144;ASN 156
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
                     
GLY 146

1qd6CHIS 142;SER 144;ASN 156
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
                     
GLY 146

1qd6DHIS 142;SER 144;ASN 156
SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
                     
GLY 146


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p.719
[7]Fig.4, p.10020-10022
[8]p.97-99
[9]p.714-716
[10]p.483-484
[11]p.1965-1966

references
[1]
CommentsACTIVE SITE SER-164, AND PARTIAL PROTEIN SEQUENCE.
PubMed ID2040286
JournalEur J Biochem
Year1991
Volume198
Pages247-53
AuthorsHorrevoets AJ, Verheij HM, de Haas GH
TitleInactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine.
Related Swiss-protP0A921
[2]
PubMed ID7589423
JournalFEBS Lett
Year1995
Volume373
Pages10-2
AuthorsBlaauw M, Dekker N, Verheij HM, Kalk KH, Dijkstra BW
TitleCrystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli.
[3]
PubMed ID9843408
JournalBiochemistry
Year1998
Volume37
Pages16011-8
AuthorsUbarretxena-Belandia I, Boots JW, Verheij HM, Dekker N
TitleRole of the cofactor calcium in the activation of outer membrane phospholipase A.
[4]
PubMed ID9774546
JournalJ Struct Biol
Year1998
Volume123
Pages67-71
AuthorsBoekema EJ, Stuart M, Koning RI, Keegstra W, Brisson A, Verheij HM, Dekker N
TitleA 7.4-A projection structure of outer membrane phospholipase A from Escherichia coli by electron crystallography.
[5]
PubMed ID9921577
JournalRes Microbiol
Year1998
Volume149
Pages703-10
AuthorsBrok RG, Boots AP, Dekker N, Verheij HM, Tommassen J
TitleSequence comparison of outer membrane phospholipases A: implications for structure and for the catalytic mechanism.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 33-289.
PubMed ID10537112
JournalNature
Year1999
Volume401
Pages717-21
AuthorsSnijder HJ, Ubarretxena-Belandia I, Blaauw M, Kalk KH, Verheij HM, Egmond MR, Dekker N, Dijkstra BW
TitleStructural evidence for dimerization-regulated activation of an integral membrane phospholipase.
Related PDB1qd5,1qd6
Related Swiss-protP0A921
[7]
PubMed ID10955989
JournalBiochemistry
Year2000
Volume39
Pages10017-22
AuthorsKingma RL, Fragiathaki M, Snijder HJ, Dijkstra BW, Verheij HM, Dekker N, Egmond MR
TitleUnusual catalytic triad of Escherichia coli outer membrane phospholipase A.
[8]
PubMed ID11080680
JournalBiochim Biophys Acta
Year2000
Volume1488
Pages91-101
AuthorsSnijder HJ, Dijkstra BW
TitleBacterial phospholipase A: structure and function of an integral membrane phospholipase.
[9]
PubMed ID10692149
JournalMol Microbiol
Year2000
Volume35
Pages711-7
AuthorsDekker N
TitleOuter-membrane phospholipase A: known structure, unknown biological function.
[10]
CommentsX-ray crystallography
PubMed ID11371166
JournalJ Mol Biol
Year2001
Volume309
Pages477-89
AuthorsSnijder HJ, Kingma RL, Kalk KH, Dekker N, Egmond MR, Dijkstra BW
TitleStructural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.
Related PDB1fw2,1fw3
[11]
CommentsX-ray crystallography
PubMed ID11567087
JournalProtein Sci
Year2001
Volume10
Pages1962-9
AuthorsSnijder HJ, Van Eerde JH, Kingma RL, Kalk KH, Dekker N, Egmond MR, Dijkstra BW
TitleStructural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
Related PDB1ild,1ilz,1im0
[12]
PubMed ID11997123
JournalBiochim Biophys Acta
Year2002
Volume1561
Pages230-7
AuthorsKingma RL, Snijder HJ, Dijkstra BW, Dekker N, Egmond MR
TitleFunctional importance of calcium binding sites in outer membrane phospholipase A.
[13]
PubMed ID11959097
JournalFEBS Lett
Year2002
Volume516
Pages31-4
AuthorsKingma RL, Egmond MR
TitleSubstrate interferes with dimerisation of outer membrane phospholipase A.
[14]
PubMed ID12875844
JournalJ Mol Biol
Year2003
Volume331
Pages177-89
AuthorsBaaden M, Meier C, Sansom MS
TitleA molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.
[15]
PubMed ID12615538
JournalJ Struct Biol
Year2003
Volume141
Pages122-31
AuthorsSnijder HJ, Timmins PA, Kalk KH, Dijkstra BW
TitleDetergent organisation in crystals of monomeric outer membrane phospholipase A.

comments
For this enzyme, calcium ion is involved both in dimerization and catalysis, together with substrate ligand, according to the literature [6], [9] & [10].
Although the calcium ion is bound to the mainchain carbonyl groups of Arg147 and Ser106 from the adjacent subunit and sidechain of Ser152, to contribute to the catalysis and dimerization, it can be bound to Asp 184 (see PDB; 1qd6 & 1fw2, literature [12]).
The catalytic reaction of this enzyme proceeds as follows:
(1) Calcium ion as a cofactor polarizes the target bond, carbonyl bond, thereby facilitating the nucleophilic by Ser144.
(2) Asn156 contributes to the activity of His142, which is a general base, either by fixing the orientation of His142 or by neutralizing the positive charge on His142.
(3) His142 acts as a general base to activate the nucleophile, Ser144.
(4) Ser144 makes a nucleophilic attack on the carbonyl carbon, leading to a tetrahedral oxyanion of the transition state.
(5) This transietn intermediate is stabilized by mainchain amide of Gly146 as well as water-mediated interactions with the cofactor, calcium ion.
(6) The transient intermediate collapses to form the acyl-enzyme intermediate.
(7) A water molecule acts as a nucleophile to attack on the acyl intermediate.
According to the literature [6] & [7], the mechanism seems to be similar to that of serine proteases such as trypsin, except for the involvement of calcium ion as a cofactor.

createdupdated
2004-03-222012-10-22
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)

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