DB code: S00127

RLCP classification 1.12.38700.511 : Hydrolysis
CATH domain 2.40.230.10 : Outer membrane phospholipase (ompla); Chain C Catalytic domain
E.C. 3.1.1.4 3.1.1.32
CSA 1qd6
M-CSA 1qd6
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A921 Phospholipase A1
EC 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
NP_418265.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491621.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF02253 (PLA1)
[Graphical View]

KEGG enzyme name
phospholipase 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 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A921 PA1_ECOLI Phosphatidylcholine + H(2)O = 2-acylglycerophosphocholine + a carboxylate. Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate. Homodimer. Cell outer membrane. Note=One of the very few enzymes located there. Calcium.

KEGG Pathways
Map code Pathways E.C.
MAP00564 Glycerophospholipid metabolism 3.1.1.4 3.1.1.32
MAP00565 Ether lipid metabolism 3.1.1.4
MAP00590 Arachidonic acid metabolism 3.1.1.4
MAP00591 Linoleic acid metabolism 3.1.1.4
MAP00592 alpha-Linolenic acid metabolism 3.1.1.4 3.1.1.32

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00076 C00157 C00001 C04230 C04233 C00060 I00123 I00085 I00086
E.C. 3.1.1.4
3.1.1.32
3.1.1.4
3.1.1.32
3.1.1.4
3.1.1.32
3.1.1.4
3.1.1.32
3.1.1.4
3.1.1.32
3.1.1.4
3.1.1.32
3.1.1.4
3.1.1.32
Compound Calcium Phosphatidylcholine H2O 1-Acyl-sn-glycero-3-phosphocholine 2-Acyl-sn-glycero-3-phosphocholine Carboxylate Peptidyl-Ser-tetrahedral intermediate (with previous carboxylic-ester) Acyl-enzyme(Peptidyl-Ser-acyl group) Peptidyl-Ser-tetrahedral-intermediate
Type divalent metal (Ca2+, Mg2+) amine group,carbohydrate,lipid,phosphate group/phosphate ion H2O amine group,carbohydrate,lipid,phosphate group/phosphate ion amine group,carbohydrate,lipid,phosphate group/phosphate ion carboxyl group
ChEBI 29108
15377
PubChem 271
22247451
962
1fw2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fw3A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fw3B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ildA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ilzA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1im0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qd5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qd6C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound Unbound Unbound Unbound Transition-state-analogue:HDS
1qd6D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound Unbound Unbound Unbound Transition-state-analogue:HDS

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0A921 & literature [6], [7] & [11]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1fw2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;SER 144;ASN 156 SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) GLY 146
1fw3A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;;ASN 156 SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) S1H 144(sulfonylated) GLY 146
1fw3B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;;ASN 156 SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) S1H 144(sulfonylated) GLY 146
1ildA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;SER 144; SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) GLY 146 mutant N156A
1ilzA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;SER 144; SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) GLY 146 mutant N156A
1im0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;SER 144; SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) GLY 146 mutant N156A
1qd5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;SER 144;ASN 156 SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) GLY 146
1qd6C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 142;SER 144;ASN 156 SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site) GLY 146
1qd6D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 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
References Sections No. 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]
Resource
Comments ACTIVE SITE SER-164, AND PARTIAL PROTEIN SEQUENCE.
Medline ID
PubMed ID 2040286
Journal Eur J Biochem
Year 1991
Volume 198
Pages 247-53
Authors Horrevoets AJ, Verheij HM, de Haas GH
Title Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine.
Related PDB
Related UniProtKB P0A921
[2]
Resource
Comments
Medline ID
PubMed ID 7589423
Journal FEBS Lett
Year 1995
Volume 373
Pages 10-2
Authors Blaauw M, Dekker N, Verheij HM, Kalk KH, Dijkstra BW
Title Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9843408
Journal Biochemistry
Year 1998
Volume 37
Pages 16011-8
Authors Ubarretxena-Belandia I, Boots JW, Verheij HM, Dekker N
Title Role of the cofactor calcium in the activation of outer membrane phospholipase A.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9774546
Journal J Struct Biol
Year 1998
Volume 123
Pages 67-71
Authors Boekema EJ, Stuart M, Koning RI, Keegstra W, Brisson A, Verheij HM, Dekker N
Title A 7.4-A projection structure of outer membrane phospholipase A from Escherichia coli by electron crystallography.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9921577
Journal Res Microbiol
Year 1998
Volume 149
Pages 703-10
Authors Brok RG, Boots AP, Dekker N, Verheij HM, Tommassen J
Title Sequence comparison of outer membrane phospholipases A: implications for structure and for the catalytic mechanism.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 33-289.
Medline ID
PubMed ID 10537112
Journal Nature
Year 1999
Volume 401
Pages 717-21
Authors Snijder HJ, Ubarretxena-Belandia I, Blaauw M, Kalk KH, Verheij HM, Egmond MR, Dekker N, Dijkstra BW
Title Structural evidence for dimerization-regulated activation of an integral membrane phospholipase.
Related PDB 1qd5 1qd6
Related UniProtKB P0A921
[7]
Resource
Comments
Medline ID
PubMed ID 10955989
Journal Biochemistry
Year 2000
Volume 39
Pages 10017-22
Authors Kingma RL, Fragiathaki M, Snijder HJ, Dijkstra BW, Verheij HM, Dekker N, Egmond MR
Title Unusual catalytic triad of Escherichia coli outer membrane phospholipase A.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11080680
Journal Biochim Biophys Acta
Year 2000
Volume 1488
Pages 91-101
Authors Snijder HJ, Dijkstra BW
Title Bacterial phospholipase A: structure and function of an integral membrane phospholipase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10692149
Journal Mol Microbiol
Year 2000
Volume 35
Pages 711-7
Authors Dekker N
Title Outer-membrane phospholipase A: known structure, unknown biological function.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11371166
Journal J Mol Biol
Year 2001
Volume 309
Pages 477-89
Authors Snijder HJ, Kingma RL, Kalk KH, Dekker N, Egmond MR, Dijkstra BW
Title Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.
Related PDB 1fw2 1fw3
Related UniProtKB
[11]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11567087
Journal Protein Sci
Year 2001
Volume 10
Pages 1962-9
Authors Snijder HJ, Van Eerde JH, Kingma RL, Kalk KH, Dekker N, Egmond MR, Dijkstra BW
Title Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
Related PDB 1ild 1ilz 1im0
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11997123
Journal Biochim Biophys Acta
Year 2002
Volume 1561
Pages 230-7
Authors Kingma RL, Snijder HJ, Dijkstra BW, Dekker N, Egmond MR
Title Functional importance of calcium binding sites in outer membrane phospholipase A.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11959097
Journal FEBS Lett
Year 2002
Volume 516
Pages 31-4
Authors Kingma RL, Egmond MR
Title Substrate interferes with dimerisation of outer membrane phospholipase A.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 12875844
Journal J Mol Biol
Year 2003
Volume 331
Pages 177-89
Authors Baaden M, Meier C, Sansom MS
Title A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12615538
Journal J Struct Biol
Year 2003
Volume 141
Pages 122-31
Authors Snijder HJ, Timmins PA, Kalk KH, Dijkstra BW
Title Detergent organisation in crystals of monomeric outer membrane phospholipase A.
Related PDB
Related UniProtKB

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.

Created Updated
2004-03-22 2012-10-22