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Escherichia coli K-12 substr. MG1655 Enzyme: phosphopantetheinyl transferase



Gene: entD Accession Numbers: EG10262 (EcoCyc), b0583, ECK0575

Synonyms: enterobactin synthetase component D, enterochelin synthase D

Regulation Summary Diagram: ?

Component of: enterobactin synthase (extended summary available)

Summary:
AcpS is the founding member of a 4'-phosphopantetheinyl (P-pant) transferase protein family that includes E. coli EntD, E. coli o195 protein, and Bacillus subtilis Sfp; family members share two conserved motifs but relatively low sequence identity overall [Lambalot96].

During enterobactin biosynthesis EntD catalyzes a posttranslational modification by transferring the phosphopantetheinyl moiety of coenzyme A onto a serine side chain in both the C-terminal apo-aryl carrier protein domain of EntB, and a homologous apo-aryl carrier protein domain of EntF. Thus, EntD mediates conversion of the apo-forms of EntB and EntF to their phosphopantetheinylated holo-forms, which primes them for their roles in acyl activation and transfer during enterobactin assembly [Gehring97, Lambalot96] (see pathway enterobactin biosynthesis).

EntD has been reported to be associated with the inner leaflet of the cytoplasmic membrane [Armstrong89].

Studies have shown that overexpressed EntD (and potentially other Sfp-type phosphopantetheinyl transferases) can complement a heterologous Shewanella pfaE-deficient gene clone comprising pfaA, pfaB, pfaC and pfaD that is involved in long-chain n-3 polyunsaturated fatty acid biosynthesis [Sugihara10].

Gene Citations: [Hunt94]

Locations: cytosol, inner membrane

Map Position: [608,682 <- 609,302] (13.12 centisomes)
Length: 621 bp / 206 aa

Molecular Weight of Polypeptide: 23.259 kD (from nucleotide sequence)

pI: 6.23

Unification Links: ASAP:ABE-0002009 , CGSC:819 , DIP:DIP-9514N , EchoBASE:EB0258 , EcoGene:EG10262 , EcoliWiki:b0583 , ModBase:P19925 , OU-Microarray:b0583 , PortEco:entD , PR:PRO_000022522 , Protein Model Portal:P19925 , RefSeq:NP_415115 , RegulonDB:EG10262 , SMR:P19925 , String:511145.b0583 , UniProt:P19925

Relationship Links: InterPro:IN-FAMILY:IPR003542 , InterPro:IN-FAMILY:IPR008278 , Pfam:IN-FAMILY:PF01648 , Prints:IN-FAMILY:PR01399

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009239 - enterobactin biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA01a, Luke71]
GO:0009059 - macromolecule biosynthetic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0008897 - holo-[acyl-carrier-protein] synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, Gehring98, Gehring97]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016780 - phosphotransferase activity, for other substituted phosphate groups Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0009366 - enterobactin synthetase complex Inferred from experiment Inferred by computational analysis [GOA01a, Gehring98]
GO:0031226 - intrinsic component of plasma membrane Inferred from experiment [Armstrong89]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell structure membrane
metabolism biosynthesis of building blocks cofactors, small molecule carriers enterochelin (enterobactin)

Essentiality data for entD 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 No 37 Aerobic 7   No [Baba06, Comment 2]

Credits:
Last-Curated ? 12-Jun-2012 by Fulcher C , SRI International


Enzymatic reaction of: phosphopantetheinyl transferase

Synonyms: 4'-phosphopantetheinyl transferase EntD

apo-serine activating enzyme + coenzyme A <=> adenosine 3',5'-bisphosphate + aryl carrier protein / L-seryl-AMP synthase

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.


Enzymatic reaction of: phosphopantetheinyl transferase

Synonyms: 4'-phosphopantetheinyl transferase EntD

isochorismatase / aryl-carrier protein + coenzyme A <=> EntB isochorismatase / aryl-carrier protein + adenosine 3',5'-bisphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Summary:
The reaction of EntD with EntB showed severe substrate inhibition which was relieved by the addition of 0.5 M NaCl to the reaction mixture [Gehring97].

Inhibitors (Unknown Mechanism): isochorismatase / aryl-carrier protein [Gehring97]


Subunit of: enterobactin synthase

Synonyms: enterobactin synthetase multienzyme complex

Subunit composition of enterobactin synthase = [EntB isochorismatase / aryl-carrier protein][EntD][EntF][(EntE)2]
         phosphopantetheinyl transferase = EntD (extended summary available)
         aryl carrier protein / L-seryl-AMP synthase = EntF (extended summary available)
         2,3-dihydroxybenzoate-AMP ligase = (EntE)2 (extended summary available)

Summary:
Enterobactin contains three units of 2,3-dihydroxybenzoylserine joined in a cyclic structure by lactone linkages. Studies have suggested that the later steps of enterobactin synthesis are carried out by a multienzyme complex consisting of the entD, entE, entF and entB gene products [Hantash97].

Proteins EntB, EntD, EntE and EntF of the enterobactin synthase multienzyme complex have been purified and characterized, but no evidence has been obtained for the existence of a stable multienzyme complex. These proteins are required for the ATP-dependent conversion of three molecules each of 2,3-dihydroxybenzoate and L-serine to enterobactin [Gehring97, Gehring98, Drake06].

Proteins EntB, EntE and EntF together contain domains that comprise a nonribosomal peptide synthase (NRPS). EntE provides an adenylation domain, EntB provides an aryl carrier protein domain (located at its C-terminus), and EntF provides condensation, adenylation, peptidyl carrier protein, and chain-releasing thioesterase domains. Thus, six domains of three proteins comprise a two-module NRPS [Ehmann00]. EntD is a phosphopantetheinyl transferase that adds this cofactor to the peptidyl carrier protein domains of EntB and EntF [Gehring97]. The activities of EntE, the EntB C-terminal domain, and EntF assemble enterobactin in an iterative manner [Drake06, Ehmann00].

Credits:
Last-Curated ? 13-Jun-2012 by Fulcher C , SRI International


Enzymatic reaction of: enterobactin synthase

EC Number: 6.3.2.14

6 ATP + 3 L-serine + 3 2,3-dihydroxybenzoate <=> 6 AMP + enterobactin + 6 diphosphate + 3 H+

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.

In Pathways: superpathway of chorismate metabolism , enterobactin biosynthesis


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 74 -> 75
[Armstrong89, UniProt10]
Alternate sequence: EL → DV; UniProt: (in Ref. 3; CAB57861);
Metal-Binding-Site 107
[UniProt11a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 109
[UniProt11a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 152
[UniProt11a]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Ingrid Keseler on Tue Oct 11, 2011:
Gene start position adjusted based on computational analysis by K. Rudd.
10/20/97 Gene b0583 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10262; confirmed by SwissProt match.


References

Armstrong89: Armstrong SK, Pettis GS, Forrester LJ, McIntosh MA (1989). "The Escherichia coli enterobactin biosynthesis gene, entD: nucleotide sequence and membrane localization of its protein product." Mol Microbiol 3(6);757-66. PMID: 2526281

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

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

Drake06: Drake EJ, Nicolai DA, Gulick AM (2006). "Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain." Chem Biol 13(4);409-19. PMID: 16632253

Ehmann00: Ehmann DE, Shaw-Reid CA, Losey HC, Walsh CT (2000). "The EntF and EntE adenylation domains of Escherichia coli enterobactin synthetase: sequestration and selectivity in acyl-AMP transfers to thiolation domain cosubstrates." Proc Natl Acad Sci U S A 97(6);2509-14. PMID: 10688898

Gehring97: Gehring AM, Bradley KA, Walsh CT (1997). "Enterobactin biosynthesis in Escherichia coli: isochorismate lyase (EntB) is a bifunctional enzyme that is phosphopantetheinylated by EntD and then acylated by EntE using ATP and 2,3-dihydroxybenzoate." Biochemistry 1997;36(28);8495-503. PMID: 9214294

Gehring98: Gehring AM, Mori I, Walsh CT (1998). "Reconstitution and characterization of the Escherichia coli enterobactin synthetase from EntB, EntE, and EntF." Biochemistry 1998;37(8);2648-59. PMID: 9485415

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

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

Hantash97: Hantash FM, Ammerlaan M, Earhart CF (1997). "Enterobactin synthase polypeptides of Escherichia coli are present in an osmotic-shock-sensitive cytoplasmic locality." Microbiology 1997;143 ( Pt 1);147-56. PMID: 9025288

Hunt94: Hunt MD, Pettis GS, McIntosh MA (1994). "Promoter and operator determinants for fur-mediated iron regulation in the bidirectional fepA-fes control region of the Escherichia coli enterobactin gene system." J Bacteriol 176(13);3944-55. PMID: 8021177

Lambalot96: Lambalot RH, Gehring AM, Flugel RS, Zuber P, LaCelle M, Marahiel MA, Reid R, Khosla C, Walsh CT (1996). "A new enzyme superfamily - the phosphopantetheinyl transferases." Chem Biol 1996;3(11);923-36. PMID: 8939709

Luke71: Luke RK, Gibson F (1971). "Location of three genes concerned with the conversion of 2,3-dihydroxybenzoate into enterochelin in Escherichia coli K-12." J Bacteriol 107(2);557-62. PMID: 4939766

Sugihara10: Sugihara S, Orikasa Y, Okuyama H (2010). "The Escherichia coli highly expressed entD gene complements the pfaE deficiency in a pfa gene clone responsible for the biosynthesis of long-chain n-3 polyunsaturated fatty acids." FEMS Microbiol Lett 307(2);207-11. PMID: 20636978

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Other References Related to Gene Regulation

Chen07: Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD (2007). "Discovery of Fur binding site clusters in Escherichia coli by information theory models." Nucleic Acids Res 35(20);6762-77. PMID: 17921503

Escolar98: Escolar L, Perez-Martin J, de Lorenzo V (1998). "Coordinated repression in vitro of the divergent fepA-fes promoters of Escherichia coli by the iron uptake regulation (Fur) protein." J Bacteriol 180(9);2579-82. PMID: 9573216

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Newman99: Newman DL, Shapiro JA (1999). "Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development." Mol Microbiol 33(1);18-32. PMID: 10411720

Pettis88: Pettis GS, Brickman TJ, McIntosh MA (1988). "Transcriptional mapping and nucleotide sequence of the Escherichia coli fepA-fes enterobactin region. Identification of a unique iron-regulated bidirectional promoter." J Biol Chem 263(35);18857-63. PMID: 2974033

Vassinova00: Vassinova N, Kozyrev D (2000). "A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli." Microbiology 146 Pt 12;3171-82. PMID: 11101675

Zhang05: Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH (2005). "Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli." J Bacteriol 187(3);980-90. PMID: 15659676


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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