Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: outer membrane phospholipase



Gene: pldA Accession Numbers: EG10738 (EcoCyc), b3821, ECK3815

Synonyms: OMPLA, Outer Membrane Phospholipase A

Regulation Summary Diagram: ?

Subunit composition of outer membrane phospholipase = [PldA]2

Summary:
pldA encodes the outer membrane phospholipase A (OMPLA) protein in E.coli K-12. Purified OMPLA displays multiple lipolytic activities and is active on phospholipids, lysophosphospholipids, diglycerides and monoglycerides however in vivo the expected substrates are the phospholipids of the cell envelope [Horrevoets89, Pugsley84].

Dimerization of OMPLA is necessary for phospholipase activity [Dekker97]. Calcium binding and substrate binding modulate dimerization and enzyme activity in vitro [Dekker97]. Interactions between enzyme and the substrates acyl side chains are the predominant stabilising factor in dimerization [Stanley06a]. Although pldA is constitutively expressed, OMPLA activity is not detected under normal conditions but is induced by conditions which disturb outer membrane integrity (reviewed in [Snijder99].

OMPLA has been implicated in bacteriocin release. In E. coli strains containing a colicin producing plasmid the activity of PldA increased prior to lysis and bacteriocin release, and phosphatidylethanolamine (the major bacterial outer membrane phospholipid) was degraded [Pugsley84]. In a colicin producing E.coli pldA mutant, colicin is retained in the cytoplasm [Cavard87].

Reviews: [Dekker00, Snijder00]

Citations: [Cavard02, Burgess08, vanderWal95]

Gene Citations: [Malinverni09, Homma84]

Locations: outer membrane

Map Position: [4,002,885 -> 4,003,754] (86.28 centisomes)
Length: 870 bp / 289 aa

Molecular Weight of Polypeptide: 33.163 kD (from nucleotide sequence), 29.0 kD (experimental) [deGeus83 ]

Unification Links: ASAP:ABE-0012479 , CGSC:384 , EchoBASE:EB0731 , EcoGene:EG10738 , EcoliWiki:b3821 , ModBase:P0A921 , OU-Microarray:b3821 , PortEco:pldA , PR:PRO_000023555 , Pride:P0A921 , Protein Model Portal:P0A921 , RefSeq:NP_418265 , RegulonDB:EG10738 , SMR:P0A921 , String:511145.b3821 , UniProt:P0A921

Relationship Links: InterPro:IN-FAMILY:IPR003187 , PDB:Structure:1FW2 , PDB:Structure:1FW3 , PDB:Structure:1ILD , PDB:Structure:1ILZ , PDB:Structure:1IM0 , PDB:Structure:1QD5 , PDB:Structure:1QD6 , Pfam:IN-FAMILY:PF02253 , Prints:IN-FAMILY:PR01486

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0016042 - lipid catabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004623 - phospholipase A2 activity Inferred from experiment Author statement Inferred by computational analysis [GOA01, Snijder01, Horrevoets89]
GO:0005509 - calcium ion binding Inferred from experiment [Snijder01]
GO:0042803 - protein homodimerization activity Inferred from experiment [Snijder01, Dekker97]
GO:0004620 - phospholipase activity Inferred by computational analysis [GOA01a]
GO:0008970 - phosphatidylcholine 1-acylhydrolase activity Author statement Inferred by computational analysis [GOA01, Snijder01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0052739 - phosphatidylserine 1-acylhydrolase activity Inferred by computational analysis [GOA01]
GO:0052740 - 1-acyl-2-lysophosphatidylserine acylhydrolase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0009279 - cell outer membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Molloy00, Homma84a]
GO:0031230 - intrinsic component of cell outer membrane Inferred from experiment [Snijder01]
GO:0045203 - integral component of cell outer membrane Inferred from experiment [Homma84a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Essentiality data for pldA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Created 05-Oct-2011 by Mackie A , Macquarie University
Last-Curated ? 05-Oct-2011 by Mackie A , Macquarie University


Enzymatic reaction of: phospholipase A2 (outer membrane phospholipase)

EC Number: 3.1.1.4

an L-1-phosphatidyl-ethanolamine[periplasmic space] + H2O[periplasmic space] <=> a fatty acid[periplasmic space] + a 2-lyso-phosphatidyl-ethanolamine[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Summary:
Phosphatidylethanolamine is shown as the reactant here as it is considered to be the main lipid component of bacterial membranes. Phosphatidylcholine (the official reactant in EC 3.1.1.32) is not a component of E.coli membranes.


Enzymatic reaction of: phospholipase A1 (outer membrane phospholipase)

Synonyms: phosphatidylcholine 1-acylhydrolase

EC Number: 3.1.1.32

an L-1-phosphatidyl-ethanolamine[periplasmic space] + H2O[periplasmic space] <=> a 1-lyso-2-acyl-sn-glycero-3-phosphoethanolamine[periplasmic space] + a fatty acid[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Summary:
Phosphatidylethanolamine is shown as the reactant here as it is considered to be the main lipid component of bacterial membranes. Phosphatidylcholine (the official reactant in EC 3.1.1.32) is not a component of E.coli membranes.


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 20
[Dekker95, Homma84, UniProt11]
.
Sequence-Conflict 14 -> 15
[Daniels92, UniProt10a]
Alternate sequence: LP → FA; UniProt: (in Ref. 2; AAA67617);
Chain 21 -> 289
[UniProt09]
UniProt: Phospholipase A1;
Sequence-Conflict 30 -> 33
[deGeus84, UniProt10a]
Alternate sequence: DAPA → MTRQ; UniProt: (in Ref. 6);
Transmembrane-Region 53 -> 65
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 85 -> 99
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 106 -> 118
[UniProt10a]
UniProt: Beta stranded;
Metal-Binding-Site 126
[UniProt10a]
UniProt: Calcium 1; via carbonyl oxygen; in dimeric form;
Transmembrane-Region 129 -> 148
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 151 -> 164
[UniProt10a]
UniProt: Beta stranded;
Active-Site 162
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: probable;
Active-Site 164
[Horrevoets91, UniProt11]
UniProt: Nucleophile.
Metal-Binding-Site 167
[UniProt10a]
UniProt: Calcium 2; via carbonyl oxygen; in dimeric form;
Mutagenesis-Variant 172
[Brok94, UniProt11]
Alternate sequence: S → F; UniProt: Inactive protein.
Metal-Binding-Site 172
[UniProt10a]
UniProt: Calcium 2; in dimeric form;
Transmembrane-Region 174 -> 186
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 189 -> 198
[UniProt10a]
UniProt: Beta stranded;
Metal-Binding-Site 204
[UniProt10a]
UniProt: Calcium 3; in monomeric form;
Transmembrane-Region 217 -> 223
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 226 -> 234
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 242 -> 250
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 256 -> 265
[UniProt10a]
UniProt: Beta stranded;
Transmembrane-Region 275 -> 286
[UniProt10a]
UniProt: Beta stranded;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3821 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10738; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Brok94: Brok RG, Brinkman E, van Boxtel R, Bekkers AC, Verheij HM, Tommassen J (1994). "Molecular characterization of enterobacterial pldA genes encoding outer membrane phospholipase A." J Bacteriol 176(3);861-70. PMID: 8300539

Burgess08: Burgess NK, Dao TP, Stanley AM, Fleming KG (2008). "Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro." J Biol Chem 283(39);26748-58. PMID: 18641391

Cavard02: Cavard D (2002). "Assembly of colicin A in the outer membrane of producing Escherichia coli cells requires both phospholipase A and one porin, but phospholipase A is sufficient for secretion." J Bacteriol 184(13);3723-33. PMID: 12057969

Cavard87: Cavard D, Baty D, Howard SP, Verheij HM, Lazdunski C (1987). "Lipoprotein nature of the colicin A lysis protein: effect of amino acid substitutions at the site of modification and processing." J Bacteriol 169(5);2187-94. PMID: 3571165

Daniels92: Daniels DL, Plunkett G, Burland V, Blattner FR (1992). "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Science 1992;257(5071);771-8. PMID: 1379743

deGeus83: de Geus P, van Die I, Bergmans H, Tommassen J, de Haas G (1983). "Molecular cloning of pldA, the structural gene for outer membrane phospholipase of E. coli K12." Mol Gen Genet 190(1);150-5. PMID: 6304472

deGeus84: de Geus P, Verheij HM, Riegman NH, Hoekstra WP, de Haas GH (1984). "The pro- and mature forms of the E. coli K-12 outer membrane phospholipase A are identical." EMBO J 3(8);1799-802. PMID: 6383820

Dekker00: Dekker N (2000). "Outer-membrane phospholipase A: known structure, unknown biological function." Mol Microbiol 35(4);711-7. PMID: 10692149

Dekker95: Dekker N, Merck K, Tommassen J, Verheij HM (1995). "In vitro folding of Escherichia coli outer-membrane phospholipase A." Eur J Biochem 232(1);214-9. PMID: 7556153

Dekker97: Dekker N, Tommassen J, Lustig A, Rosenbusch JP, Verheij HM (1997). "Dimerization regulates the enzymatic activity of Escherichia coli outer membrane phospholipase A." J Biol Chem 272(6);3179-84. PMID: 9013551

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Homma84: Homma H, Kobayashi T, Chiba N, Karasawa K, Mizushima H, Kudo I, Inoue K, Ikeda H, Sekiguchi M, Nojima S (1984). "The DNA sequence encoding pldA gene, the structural gene for detergent-resistant phospholipase A of E. coli." J Biochem 96(6);1655-64. PMID: 6397464

Homma84a: Homma H, Chiba N, Kobayashi T, Kudo I, Inoue K, Ikeda H, Sekiguchi M, Nojima S (1984). "Characteristics of detergent-resistant phospholipase A overproduced in E. coli cells bearing its cloned structural gene." J Biochem 96(6);1645-53. PMID: 6397463

Horrevoets89: Horrevoets AJ, Hackeng TM, Verheij HM, Dijkman R, de Haas GH (1989). "Kinetic characterization of Escherichia coli outer membrane phospholipase A using mixed detergent-lipid micelles." Biochemistry 28(3);1139-47. PMID: 2653433

Horrevoets91: Horrevoets AJ, Verheij HM, de Haas GH (1991). "Inactivation of Escherichia coli outer-membrane phospholipase A by the affinity label hexadecanesulfonyl fluoride. Evidence for an active-site serine." Eur J Biochem 198(1);247-53. PMID: 2040286

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Malinverni09: Malinverni JC, Silhavy TJ (2009). "An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane." Proc Natl Acad Sci U S A 106(19):8009-14. PMID: 19383799

Molloy00: Molloy MP, Herbert BR, Slade MB, Rabilloud T, Nouwens AS, Williams KL, Gooley AA (2000). "Proteomic analysis of the Escherichia coli outer membrane." Eur J Biochem 267(10);2871-81. PMID: 10806384

Pugsley84: Pugsley AP, Schwartz M (1984). "Colicin E2 release: lysis, leakage or secretion? Possible role of a phospholipase." EMBO J 3(10);2393-7. PMID: 6389120

Snijder00: Snijder HJ, Dijkstra BW (2000). "Bacterial phospholipase A: structure and function of an integral membrane phospholipase." Biochim Biophys Acta 1488(1-2);91-101. PMID: 11080680

Snijder01: Snijder HJ, Kingma RL, Kalk KH, Dekker N, Egmond MR, Dijkstra BW (2001). "Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli." J Mol Biol 309(2);477-89. PMID: 11371166

Snijder99: Snijder HJ, Ubarretxena-Belandia I, Blaauw M, Kalk KH, Verheij HM, Egmond MR, Dekker N, Dijkstra BW (1999). "Structural evidence for dimerization-regulated activation of an integral membrane phospholipase." Nature 401(6754);717-21. PMID: 10537112

Stanley06a: Stanley AM, Chuawong P, Hendrickson TL, Fleming KG (2006). "Energetics of outer membrane phospholipase A (OMPLA) dimerization." J Mol Biol 358(1);120-31. PMID: 16497324

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

vanderWal95: van der Wal FJ, Luirink J, Oudega B (1995). "Bacteriocin release proteins: mode of action, structure, and biotechnological application." FEMS Microbiol Rev 17(4);381-99. PMID: 8845188

Other References Related to Gene Regulation

Harley87: Harley CB, Reynolds RP (1987). "Analysis of E. coli promoter sequences." Nucleic Acids Res 15(5);2343-61. PMID: 3550697


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc14.