S00127
type: Enzyme
rlcp: p511
cath: Outer membrane phospholipase (ompla); Chain C
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32
csa: 1qd6
uniprot: P0A921
kegg enzyme: phospholipase A2
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/3.1.1.4
kegg enzyme: lecithinase A
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/3.1.1.4
kegg enzyme: phosphatidase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/3.1.1.4
kegg enzyme: phosphatidolipase
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/3.1.1.4
kegg enzyme: phospholipase A
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/3.1.1.4
kegg enzyme: phospholipase A1
  type: KeggEnzyme
  ec: https://purl.uniprot.org/enzyme/3.1.1.32
kegg pathway: Glycerophospholipid metabolism
kegg pathway: Ether lipid metabolism
kegg pathway: Arachidonic acid metabolism
kegg pathway: Linoleic acid metabolism
kegg pathway: alpha-Linolenic acid metabolism
kegg cofactor: Calcium
kegg substrate: Phosphatidylcholine
kegg substrate: H2O
kegg product: 1-Acyl-sn-glycero-3-phosphocholine
kegg product: 2-Acyl-sn-glycero-3-phosphocholine
kegg product: Carboxylate
kegg intermediate: Peptidyl-Ser-tetrahedral intermediate (with previous carboxylic-ester)
kegg intermediate: Acyl-enzyme(Peptidyl-Ser-acyl group)
kegg intermediate: Peptidyl-Ser-tetrahedral-intermediate
pdb: 1fw2A
pdb: 1fw3A
pdb: 1fw3B
pdb: 1ildA
pdb: 1ilzA
pdb: 1im0A
pdb: 1qd5A
pdb: 1qd6C
pdb: 1qd6D
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1fw2A
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1fw3A
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1fw3B
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1ildA
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1ilzA
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1im0A
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1qd5A
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1qd6C
pdb bound state: Unbound
  compound: Phosphatidylcholine
  pdb: 1qd6D
pdb bound state: Unbound
  compound: Calcium
  pdb: 1fw2A
pdb bound state: Unbound
  compound: Calcium
  pdb: 1fw3A
pdb bound state: Unbound
  compound: Calcium
  pdb: 1fw3B
pdb bound state: Unbound
  compound: Calcium
  pdb: 1ildA
pdb bound state: Unbound
  compound: Calcium
  pdb: 1ilzA
pdb bound state: Unbound
  compound: Calcium
  pdb: 1im0A
pdb bound state: Unbound
  compound: Calcium
  pdb: 1qd5A
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1fw2A
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1fw3A
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1fw3B
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1ildA
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1ilzA
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1im0A
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1qd5A
pdb bound state: Unbound
  compound: 1-Acyl-sn-glycero-3-phosphocholine
  pdb: 1qd6C
active site residues resources: Unusual catalytic triad of Escherichia coli outer membrane phospholipase A.
active site residues resources: Bacterial phospholipase A: structure and function of an integral membrane phospholipase.
active site residues resources: Functional importance of calcium binding sites in outer membrane phospholipase A.
active site residues resources: P0A921
references: Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine.
references: Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli.
references: Role of the cofactor calcium in the activation of outer membrane phospholipase A.
references: A 7.4-A projection structure of outer membrane phospholipase A from Escherichia coli by electron crystallography.
references: Sequence comparison of outer membrane phospholipases A: implications for structure and for the catalytic mechanism.
references: Structural evidence for dimerization-regulated activation of an integral membrane phospholipase.
references: Unusual catalytic triad of Escherichia coli outer membrane phospholipase A.
references: Bacterial phospholipase A: structure and function of an integral membrane phospholipase.
references: Outer-membrane phospholipase A: known structure, unknown biological function.
references: Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.
references: Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
references: Functional importance of calcium binding sites in outer membrane phospholipase A.
references: Substrate interferes with dimerisation of outer membrane phospholipase A.
references: A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.
references: Detergent organisation in crystals of monomeric outer membrane phospholipase A.
comment: 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.

Outer membrane phospholipase (ompla); Chain C
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/2.40.230.10
catalytic domain: index.html

Glycerophospholipid metabolism
type: KeggPathway
references: KEGG:MAP00564
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32

Ether lipid metabolism
type: KeggPathway
references: KEGG:MAP00565
ec: https://purl.uniprot.org/enzyme/3.1.1.4

Arachidonic acid metabolism
type: KeggPathway
references: KEGG:MAP00590
ec: https://purl.uniprot.org/enzyme/3.1.1.4

Linoleic acid metabolism
type: KeggPathway
references: KEGG:MAP00591
ec: https://purl.uniprot.org/enzyme/3.1.1.4

alpha-Linolenic acid metabolism
type: KeggPathway
references: KEGG:MAP00592
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32

Calcium
type: KeggCofactor
references: KEGG:C00076
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:29108
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Phosphatidylcholine
type: KeggSubstrate
references: KEGG:C00157
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32
compound type: amine group
compound type: carbohydrate
compound type: lipid
compound type: phosphate group/phosphate ion

H2O
type: KeggSubstrate
references: KEGG:C00001
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1-Acyl-sn-glycero-3-phosphocholine
type: KeggProduct
references: KEGG:C04230
ec: https://purl.uniprot.org/enzyme/3.1.1.4
compound type: amine group
compound type: carbohydrate
compound type: lipid
compound type: phosphate group/phosphate ion

2-Acyl-sn-glycero-3-phosphocholine
type: KeggProduct
references: KEGG:C04233
ec: https://purl.uniprot.org/enzyme/3.1.1.32
compound type: amine group
compound type: carbohydrate
compound type: lipid
compound type: phosphate group/phosphate ion

Carboxylate
type: KeggProduct
references: KEGG:C00060
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32
compound type: carboxyl group

Peptidyl-Ser-tetrahedral intermediate (with previous carboxylic-ester)
type: KeggIntermediate
references: KEGG:I00123
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32

Acyl-enzyme(Peptidyl-Ser-acyl group)
type: KeggIntermediate
references: KEGG:I00085
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32

Peptidyl-Ser-tetrahedral-intermediate
type: KeggIntermediate
references: KEGG:I00086
ec: https://purl.uniprot.org/enzyme/3.1.1.4
ec: https://purl.uniprot.org/enzyme/3.1.1.32

1fw2A
type: Pdb
references: 1fw2
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fw2
catalytic residue: HIS 142;SER 144;ASN 156
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
main chain in catalysis: GLY 146

1fw3A
type: Pdb
references: 1fw3
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fw3
catalytic residue: HIS 142; ;ASN 156
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
modified residue: S1H 144(sulfonylated)
main chain in catalysis: GLY 146

1fw3B
type: Pdb
references: 1fw3
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fw3
catalytic residue: HIS 142; ;ASN 156
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
modified residue: S1H 144(sulfonylated)
main chain in catalysis: GLY 146

1ildA
type: Pdb
references: 1ild
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ild
catalytic residue: HIS 142;SER 144;
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
main chain in catalysis: GLY 146
comment: mutant N156A

1ilzA
type: Pdb
references: 1ilz
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ilz
catalytic residue: HIS 142;SER 144;
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
main chain in catalysis: GLY 146
comment: mutant N156A

1im0A
type: Pdb
references: 1im0
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1im0
catalytic residue: HIS 142;SER 144;
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
main chain in catalysis: GLY 146
comment: mutant N156A

1qd5A
type: Pdb
references: 1qd5
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qd5
catalytic residue: HIS 142;SER 144;ASN 156
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
main chain in catalysis: GLY 146

1qd6C
type: Pdb
references: 1qd6
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qd6
catalytic residue: HIS 142;SER 144;ASN 156
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
main chain in catalysis: GLY 146

1qd6D
type: Pdb
references: 1qd6
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qd6
catalytic residue: HIS 142;SER 144;ASN 156
cofactor binding residue: SER 106;SER 152;ARG 147(Catalytic calcium binding);ASP 184(calcium 2nd site)
main chain in catalysis: GLY 146

Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine.
type: BibliographicResource
comment: ACTIVE SITE SER-164, AND PARTIAL PROTEIN SEQUENCE.
references: http://www.ncbi.nlm.nih.gov/pubmed/2040286
journal: Eur J Biochem
volume: 198
pages: 247-53
published year: 1991
authors:
  item: Horrevoets AJ
  item: Verheij HM
  item: de Haas GH
references: P0A921

Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7589423
journal: FEBS Lett
volume: 373
pages: 10-2
published year: 1995
authors:
  item: Blaauw M
  item: Dekker N
  item: Verheij HM
  item: Kalk KH
  item: Dijkstra BW

Role of the cofactor calcium in the activation of outer membrane phospholipase A.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9843408
journal: Biochemistry
volume: 37
pages: 16011-8
published year: 1998
authors:
  item: Ubarretxena-Belandia I
  item: Boots JW
  item: Verheij HM
  item: Dekker N

A 7.4-A projection structure of outer membrane phospholipase A from Escherichia coli by electron crystallography.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9774546
journal: J Struct Biol
volume: 123
pages: 67-71
published year: 1998
authors:
  item: Boekema EJ
  item: Stuart M
  item: Koning RI
  item: Keegstra W
  item: Brisson A
  item: Verheij HM
  item: Dekker N

Sequence comparison of outer membrane phospholipases A: implications for structure and for the catalytic mechanism.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9921577
journal: Res Microbiol
volume: 149
pages: 703-10
published year: 1998
authors:
  item: Brok RG
  item: Boots AP
  item: Dekker N
  item: Verheij HM
  item: Tommassen J

Structural evidence for dimerization-regulated activation of an integral membrane phospholipase.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 33-289.
references: http://www.ncbi.nlm.nih.gov/pubmed/10537112
journal: Nature
volume: 401
pages: 717-21
published year: 1999
authors:
  item: Snijder HJ
  item: Ubarretxena-Belandia I
  item: Blaauw M
  item: Kalk KH
  item: Verheij HM
  item: Egmond MR
  item: Dekker N
  item: Dijkstra BW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A921

Unusual catalytic triad of Escherichia coli outer membrane phospholipase A.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10955989
journal: Biochemistry
volume: 39
pages: 10017-22
published year: 2000
authors:
  item: Kingma RL
  item: Fragiathaki M
  item: Snijder HJ
  item: Dijkstra BW
  item: Verheij HM
  item: Dekker N
  item: Egmond MR

Bacterial phospholipase A: structure and function of an integral membrane phospholipase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11080680
journal: Biochim Biophys Acta
volume: 1488
pages: 91-101
published year: 2000
authors:
  item: Snijder HJ
  item: Dijkstra BW

Outer-membrane phospholipase A: known structure, unknown biological function.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10692149
journal: Mol Microbiol
volume: 35
pages: 711-7
published year: 2000
authors:
  item: Dekker N

Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/11371166
journal: J Mol Biol
volume: 309
pages: 477-89
published year: 2001
authors:
  item: Snijder HJ
  item: Kingma RL
  item: Kalk KH
  item: Dekker N
  item: Egmond MR
  item: Dijkstra BW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/11567087
journal: Protein Sci
volume: 10
pages: 1962-9
published year: 2001
authors:
  item: Snijder HJ
  item: Van Eerde JH
  item: Kingma RL
  item: Kalk KH
  item: Dekker N
  item: Egmond MR
  item: Dijkstra BW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Functional importance of calcium binding sites in outer membrane phospholipase A.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11997123
journal: Biochim Biophys Acta
volume: 1561
pages: 230-7
published year: 2002
authors:
  item: Kingma RL
  item: Snijder HJ
  item: Dijkstra BW
  item: Dekker N
  item: Egmond MR

Substrate interferes with dimerisation of outer membrane phospholipase A.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11959097
journal: FEBS Lett
volume: 516
pages: 31-4
published year: 2002
authors:
  item: Kingma RL
  item: Egmond MR

A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12875844
journal: J Mol Biol
volume: 331
pages: 177-89
published year: 2003
authors:
  item: Baaden M
  item: Meier C
  item: Sansom MS

Detergent organisation in crystals of monomeric outer membrane phospholipase A.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12615538
journal: J Struct Biol
volume: 141
pages: 122-31
published year: 2003
authors:
  item: Snijder HJ
  item: Timmins PA
  item: Kalk KH
  item: Dijkstra BW

TransitionStateAnalogue
compound: Peptidyl-Ser-tetrahedral-intermediate
pdb: 1qd6C
ligand het code: HDS

TransitionStateAnalogue
compound: Peptidyl-Ser-tetrahedral-intermediate
pdb: 1qd6D
ligand het code: HDS

ReferenceForCatalyticMechanism
reference index: 6
reference section: p.719

ReferenceForCatalyticMechanism
reference index: 7
reference section: Fig.4, p.10020-10022

ReferenceForCatalyticMechanism
reference index: 8
reference section: p.97-99

ReferenceForCatalyticMechanism
reference index: 9
reference section: p.714-716

ReferenceForCatalyticMechanism
reference index: 10
reference section: p.483-484

ReferenceForCatalyticMechanism
reference index: 11
reference section: p.1965-1966