P0A921 (PA1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phospholipase A1
EC=3.1.1.32
EC=3.1.1.4

Alternative name(s):
Detergent-resistant phospholipase A
Short name=DR-phospholipase A
Outer membrane phospholipase A
Short name=OM PLA
Short name=OMPLA
Phosphatidylcholine 1-acylhydrolase

Gene names

Name:	pldA
Ordered Locus Names:	b3821, JW3794

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	289 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Has broad substrate specificity including hydrolysis of phosphatidylcholine with phospholipase A2 (EC 3.1.1.4) and phospholipase A1 (EC 3.1.1.32) activities. Strong expression leads to outer membrane breakdown and cell death; is dormant in normal growing cells. Required for efficient secretion of bacteriocins.
Catalytic activity	Phosphatidylcholine + H2O = 2-acylglycerophosphocholine + a carboxylate. Phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
Cofactor	Binds 1 calcium ion per monomer. In the dimeric form the calcium is bound by different amino acids with binding of each calcium shared with ligands coming from each monomer (Arg-167 and Ser-172 from 1 monomer, Ser-126 of the other). The calcium ion may have a role in catalysis. Ref.13
Enzyme regulation	By membrane damage, for example, by phage-induced lysis or temperature shock. The protein is inactive in the monomeric form and active in the dimeric form; calcium is essential for dimer stability. Ref.11 Ref.12
Subunit structure	Homodimer; dimerization is reversible, and the dimeric form is the active one. Ref.11 Ref.12 Ref.13
Subcellular location	Cell outer membrane; Multi-pass membrane protein. Note: One of the very few enzymes located there. Ref.8
Sequence similarities	Belongs to the phospholipase A1 family.

Ontologies

Keywords
Biological process	Lipid degradation Lipid metabolism
Cellular component	Cell membrane Cell outer membrane Membrane
Domain	Signal Transmembrane Transmembrane beta strand
Ligand	Calcium Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	lipid catabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	integral to cell outer membrane Inferred from direct assay Ref.8. Source: EcoCyc plasma membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	1-acyl-2-lysophosphatidylserine acylhydrolase activity Inferred from electronic annotation. Source: EC calcium ion binding Inferred from direct assay Ref.14. Source: UniProtKB phosphatidylcholine 1-acylhydrolase activity Traceable author statement Ref.14. Source: UniProtKB phosphatidylserine 1-acylhydrolase activity Inferred from electronic annotation. Source: EC phospholipase A2 activity Traceable author statement Ref.14. Source: UniProtKB protein homodimerization activity Inferred from direct assay Ref.14. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
yhjC	P37641	1	EBI-1119179,EBI-849303

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 20

20

Ref.1 Ref.5

Chain

21 – 289

269

Phospholipase A1

PRO_0000021983

Regions

Topological domain

21 – 52

32

Periplasmic

Transmembrane

53 – 65

13

Beta stranded

Topological domain

66 – 84

19

Extracellular

Transmembrane

85 – 99

15

Beta stranded

Topological domain

100 – 105

6

Periplasmic

Transmembrane

106 – 118

13

Beta stranded

Topological domain

119 – 128

10

Extracellular

Transmembrane

129 – 148

20

Beta stranded

Topological domain

149 – 150

2

Periplasmic

Transmembrane

151 – 164

14

Beta stranded

Topological domain

165 – 173

9

Extracellular

Transmembrane

174 – 186

13

Beta stranded

Topological domain

187 – 188

2

Periplasmic

Transmembrane

189 – 198

10

Beta stranded

Topological domain

199 – 216

18

Extracellular

Transmembrane

217 – 223

7

Beta stranded

Topological domain

224 – 225

2

Periplasmic

Transmembrane

226 – 234

9

Beta stranded

Topological domain

235 – 241

7

Extracellular

Transmembrane

242 – 250

9

Beta stranded

Topological domain

251 – 255

5

Periplasmic

Transmembrane

256 – 265

10

Beta stranded

Topological domain

266 – 274

9

Extracellular

Transmembrane

275 – 286

12

Beta stranded

Topological domain

287 – 289

3

Periplasmic

Sites

Active site

162

1

Proton acceptor Probable

Active site

164

1

Nucleophile Ref.10

Metal binding

126

1

Calcium 1; via carbonyl oxygen; in dimeric form

Metal binding

167

1

Calcium 2; via carbonyl oxygen; in dimeric form

Metal binding

172

1

Calcium 2; in dimeric form

Metal binding

204

1

Calcium 3; in monomeric form

Experimental info

Mutagenesis

172

1

S → F: Inactive protein. Ref.9

Sequence conflict

14 – 15

2

LP → FA in AAA67617. Ref.2

Sequence conflict

30 – 33

4

DAPA → MTRQ Ref.6

Secondary structure

1

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289

Helix Strand Turn

Details...

Helix

38 – 43

6

Beta strand

52 – 54

3

Beta strand

59 – 67

9

Turn

70 – 75

6

Helix

79 – 81

3

Beta strand

84 – 99

16

Turn

100 – 102

3

Beta strand

106 – 118

13

Helix

123 – 125

3

Beta strand

129 – 148

20

Beta strand

151 – 164

14

Beta strand

169 – 171

3

Beta strand

174 – 186

13

Beta strand

189 – 193

5

Beta strand

196 – 198

3

Helix

208 – 212

5

Beta strand

217 – 223

7

Beta strand

226 – 234

9

Turn

236 – 238

3

Beta strand

241 – 254

14

Beta strand

256 – 265

10

Beta strand

267 – 269

3

Turn

270 – 273

4

Beta strand

275 – 285

11

Sequences

	Sequence		Length	Mass (Da)
	P0A921 [UniParc]. Last modified July 19, 2005. Version 1. Checksum: A688AD32AA60F218	FASTA	289	33,163
	10 20 30 40 50 60 MRTLQGWLLP VFMLPMAVYA QEATVKEVHD APAVRGSIIA NMLQEHDNPF TLYPYDTNYL 70 80 90 100 110 120 IYTQTSDLNK EAIASYDWAE NARKDEVKFQ LSLAFPLWRG ILGPNSVLGA SYTQKSWWQL 130 140 150 160 170 180 SNSEESSPFR ETNYEPQLFL GFATDYRFAG WTLRDVEMGY NHDSNGRSDP TSRSWNRLYT 190 200 210 220 230 240 RLMAENGNWL VEVKPWYVVG NTDDNPDITK YMGYYQLKIG YHLGDAVLSA KGQYNWNTGY 250 260 270 280 GGAELGLSYP ITKHVRLYTQ VYSGYGESLI DYNFNQTRVG VGVMLNDLF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The DNA sequence encoding pldA gene, the structural gene for detergent-resistant phospholipase A of E. coli." Homma H., Kobayashi T., Chiba N., Karasawa K., Mizushima H., Kudo I., Inoue K., Ikeda H., Sekiguchi M., Nojima S. J. Biochem. 96:1655-1664(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 21-30. Strain: K12.
[2]	"Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R. Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 14-15. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"In vitro folding of Escherichia coli outer-membrane phospholipase A." Dekker N., Merck K., Tommassen J., Verheij H.M. Eur. J. Biochem. 232:214-219(1995) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 21-24. Strain: K12.
[6]	"The pro- and mature forms of the E. coli K-12 outer membrane phospholipase A are identical." de Geus P., Verheij H.M., Riegman N.H., Hoekstra W.P.M., de Haas G.H. EMBO J. 3:1799-1802(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 30-289. Strain: K12.
[7]	"The recQ gene of Escherichia coli K12: primary structure and evidence for SOS regulation." Irino N., Nakayama K., Nakayama H. Mol. Gen. Genet. 205:298-304(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 174-289. Strain: K12.
[8]	"Characteristics of detergent-resistant phospholipase A overproduced in E. coli cells bearing its cloned structural gene." Homma H., Chiba N., Kobayashi T., Kudo I., Inoue K., Ikeda H., Sekiguchi M., Nojima S. J. Biochem. 96:1645-1653(1984) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION. Strain: K12.
[9]	"Molecular characterization of enterobacterial pldA genes encoding outer membrane phospholipase A." Brok R.G.P.M., Brinkman E., van Boxtel R., Bekkers A.C.A.P., Verheij H.M., Tommassen J. J. Bacteriol. 176:861-870(1994) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF SER-172.
[10]	"Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine." Horrevoets A.J.G., Verheij H.M., de Haas G.H. Eur. J. Biochem. 198:247-253(1991) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITE SER-164, PARTIAL PROTEIN SEQUENCE.
[11]	"Dimerization regulates the enzymatic activity of Escherichia coli outer membrane phospholipase A." Dekker N., Tommassen J., Lustig A., Rosenbusch J.P., Verheij H.M. J. Biol. Chem. 272:3179-3184(1997) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, ENZYME REGULATION.
[12]	"Bacteriocin release protein triggers dimerization of outer membrane phospholipase A in vivo." Dekker N., Tommassen J., Verheij H.M. J. Bacteriol. 181:3281-3283(1999) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, ENZYME REGULATION.
[13]	"Structural evidence for dimerization-regulated activation of an integral membrane phospholipase." Snijder H.J., Ubarretxena-Belandia I., Blaauw M., Kalk K.H., Verheij H.M., Egmond M.R., Dekker N., Dijkstra B.W. Nature 401:717-721(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 33-289 IN MONOMERIC AND DIMERIC FORM, COFACTOR, SUBUNIT.
[14]	"Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli." Snijder H.J., Kingma R.L., Kalk K.H., Dekker N., Egmond M.R., Dijkstra B.W. J. Mol. Biol. 309:477-489(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 21-289 IN MONOMERIC AND DIMERIC FORM IN THE PRESENCE AND ABSENCE OF CALCIUM.
[15]	"Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad." Snijder H.J., Van Eerde J.H., Kingma R.L., Kalk K.H., Dekker N., Egmond M.R., Dijkstra B.W. Protein Sci. 10:1962-1969(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 21-289 OF MUTANT ALA-156.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X02143 Genomic DNA. Translation: CAA26081.1.
M87049 Genomic DNA. Translation: AAA67617.1.
U00096 Genomic DNA. Translation: AAC76824.1.
AP009048 Genomic DNA. Translation: BAE77480.1.
M30198 Genomic DNA. Translation: AAA24516.1.

PIR

PSECA1. A22133.

RefSeq

NP_418265.1. NC_000913.2.
YP_491621.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FW2	X-ray	2.60	A	21-289	[»]
1FW3	X-ray	2.80	A/B	21-289	[»]
1ILD	X-ray	2.80	A	21-289	[»]
1ILZ	X-ray	2.50	A	21-289	[»]
1IM0	X-ray	2.98	A	21-289	[»]
1QD5	X-ray	2.17	A	21-289	[»]
1QD6	X-ray	2.10	A/B	33-45	[»]
			C/D	50-289	[»]

ProteinModelPortal

P0A921.

SMR

P0A921. Positions 33-289.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A921. 12 interactions.

STRING

511145.b3821.

Proteomic databases

PaxDb

P0A921.

PRIDE

P0A921.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76824; AAC76824; b3821.
BAE77480; BAE77480; BAE77480.

GeneID

12930309.
948307.

KEGG

ecj:Y75_p3357.
eco:b3821.

PATRIC

32123143. VBIEscCol129921_3937.

Organism-specific databases

EchoBASE

EB0731.

EcoGene

EG10738. pldA.

Phylogenomic databases

eggNOG

COG2829.

HOGENOM

HOG000288150.

KO

K01058.

OMA

YNHRQTR.

ProtClustDB

PRK10763.

Enzyme and pathway databases

BioCyc

EcoCyc:MONOMER0-341.
ECOL316407:JW3794-MONOMER.
MetaCyc:MONOMER0-341.

Gene expression databases

Genevestigator

P0A921.

Family and domain databases

Gene3D

2.40.230.10. 1 hit.

InterPro

IPR003187. PLipase_A1.
[Graphical view]

Pfam

PF02253. PLA1. 1 hit.
[Graphical view]

PRINTS

PR01486. PHPHLIPASEA1.

SUPFAM

SSF56931. PLA1. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0A921.

Entry information

Entry name

PA1_ECOLI

Accession

Primary (citable) accession number: P0A921
Secondary accession number(s): P00631, Q2M8C6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 19, 2005
Last modified:	May 1, 2013
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program