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Escherichia coli K-12 substr. MG1655 Enzyme: penicillin-binding protein 6



Gene: dacC Accession Numbers: EG10203 (EcoCyc), b0839, ECK0829

Synonyms: D-alanyl-D-alanine carboxypeptidase, PBP6

Regulation Summary Diagram: ?

Summary:
PBP6 is a penicillin-binding protein that is required for proper cell morphology and provides some resistance to penicillin [vanderLinden92, Santos02, BroomeSmith82]. It is one of four DD-carboxypeptidase low-molecular weight PBPs in Escherichia coli (along with PBP4, PBP5 and DacD) that modify peptidoglycans through the removal of the terminal D-alanine from pentapeptide side chains [Matsuhashi79, Baquero96].

PBP6 contains the β-lactam/penicillin-binding domain motif sequences SxxK (SLTK), [S/Y]xN (SGN), and [K/H][T/S]G (KTG) [Baquero96]. The carboxy-terminus of PBP6 is capable of forming an alpha helix and interacts with membranes chiefly through hydrophobic forces [Harris97, Siligardi97, Harris98b, Harris02]. Deletion of this membrane-anchoring portion of the protein produces soluble PBP6 [vanderLinden92]. Whereas overexpression of native PBP6 results in membrane vesicles in the cystoplasm, overexpression of this soluble variant yields inclusion bodies [vanderLinden92]. Both forms of PBP6 can be purified with Procion rubine MX-B and subsequently bind stoichiometrically with benzylpenicillin [vanderLinden92]. PBP6 fractionates with PBP4 and PBP7/8 or just with PBP7/8 in membrane vesicles depending on the method used [Leidenix89].

Despite being part of a family of D-alanine carboxypeptidases, PBP6 lacks detectable activity against bisacetyl-L-lysine-D-alanyl-D-alanine and other test substrates [vanderLinden92], though previous assays detected this activity as well as transpeptidase activity in which the terminal D-alanine is exchanged for glycine [Amanuma80, Amanuma84]. PBP6 was also shown to bind penicillin G [Amanuma80, Amanuma84].

Deletions in dacC are viable and had no obvious growth defects, though they are slightly penicillin sensitive [BroomeSmith82]. dacC and dacC dacA mutants are viable, though they show defects in morphology and cell division when bolA, which is required for dacC expression upon entry into stationary phase, is overexpressed [BroomeSmith85, Santos02, Aldea89]. A complete deletion of dacA-D is also viable, as is a strain lacking eight of the known penicillin-binding protein genes, dacC among them [Baquero96, Denome99]. A mrcA dacB dacA dacC AmpC, dacA dacB dacC, dacA pbpG dacC, or yrfE yrfF mrcA dacA dacB dacC pbpG ampC ampH mutant has abnormal cellular morphology [Nelson00, Nelson01, dePedro03]. Inhibition of FtsZ by SulA in a dacA dacB mutant results in growth of spiral-shaped cells [Varma04]. Overexpression of dacC allows cell division in ftsI23 mutants [Begg90], but leads to cell lysis during early exponential growth [Nelson01]. Levels of PBP6 are greatly diminished in minicells [Obermann94]. Attachment of the C-terminal membrane anchor of PBP6 to a mutant PBP5 with its own C-terminal anchor removed can complement the morphological defects of the PBP5 mutant [Nelson02]. Combining the N-terminal domain of PBP5 with the C-terminal β-sheet of PBP6 also resulted in a functional protein able to complement a dacA mutant [Nelson02].

The amount of PBP6 found in cells increases during stationary phase [Buchanan82]. Expression of dacC is induced upon entry into stationary phase by BolA [Santos02]. Expression of dacC is also regulated by LRP [Tani02]. Expression of dacC was upregulated under basic conditions with oxygen limitation [Hayes06]. Expression of dacC increased upon treatment with cefsulodin and amdinocillin [Laubacher08].

Reviews: [Ghosh08, Scheffers05, Holtje98, Nanninga98]

Citations: [Tamura76, Spratt77, Spratt80, Pratt81, BroomeSmith88, Lange91a, Rawlings93, Meberg01, Ghosh03]

Locations: inner membrane

Map Position: [879,950 -> 881,152] (18.97 centisomes)
Length: 1203 bp / 400 aa

Molecular Weight of Polypeptide: 43.609 kD (from nucleotide sequence), 40.0 kD (experimental) [Amanuma80 ]

Unification Links: ASAP:ABE-0002860 , CGSC:34706 , EchoBASE:EB0199 , EcoGene:EG10203 , EcoliWiki:b0839 , Mint:MINT-6478097 , ModBase:P08506 , OU-Microarray:b0839 , PortEco:dacC , PR:PRO_000022394 , Pride:P08506 , Protein Model Portal:P08506 , RefSeq:NP_415360 , RegulonDB:EG10203 , SMR:P08506 , String:511145.b0839 , Swiss-Model:P08506 , UniProt:P08506

Relationship Links: InterPro:IN-FAMILY:IPR001967 , InterPro:IN-FAMILY:IPR012338 , InterPro:IN-FAMILY:IPR012907 , InterPro:IN-FAMILY:IPR015956 , InterPro:IN-FAMILY:IPR018044 , PDB:Structure:3IT9 , PDB:Structure:3ITA , PDB:Structure:3ITB , Pfam:IN-FAMILY:PF00768 , Pfam:IN-FAMILY:PF07943 , Prints:IN-FAMILY:PR00725 , Smart:IN-FAMILY:SM00936

In Paralogous Gene Group: 169 (4 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008360 - regulation of cell shape Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Varma04, Nelson01, Nelson00]
GO:0009252 - peptidoglycan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, Amanuma80, Amanuma84]
GO:0042493 - response to drug Inferred from experiment [BroomeSmith82]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004180 - carboxypeptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Amanuma80, Amanuma84]
GO:0008658 - penicillin binding Inferred from experiment [Amanuma80, Amanuma84]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0009002 - serine-type D-Ala-D-Ala carboxypeptidase activity Inferred by computational analysis [GOA01, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005887 - integral component of plasma membrane Inferred from experiment [Spratt77]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell processes cell division
cell processes protection drug resistance/sensitivity

Essentiality data for dacC 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]

Enzymatic reaction of: D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6)

EC Number: 3.4.16.4

a lipid II[periplasmic space] + H2O[periplasmic space] <=> a N-acetylglucosamine--N-acetylmuramyl-(tetrapeptide) pyrophosphoryl-undecaprenol[periplasmic space] + D-alanine[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:
There is contradictory evidence regarding whether PBP6 is actually capable of performing this reaction [vanderLinden92, Amanuma80, Amanuma84].

T(opt): 37 °C [Hsieh06, BRENDA14, Josephine06]

pH(opt): 7.2 [BRENDA14, Hsieh06], 8 [BRENDA14, Josephine06], 8.5 [BRENDA14, Josephine06], 9 [BRENDA14, Stefanova02]


Sequence Features

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 27 PBP6 signal sequence
[Waxman82, Pratt81a]
 
Chain 28 -> 400  
[UniProt09]
UniProt: D-alanyl-D-alanine carboxypeptidase dacC;
Active-Site 66  
[UniProt10]
UniProt: Acyl-ester intermediate; Non-Experimental Qualifier: by similarity;
Active-Site 66, 67, 68, 69, 132, 133, 134, 235, 236, 237 PBP6 penicillin-binding domain
[Baquero96]
 
Active-Site 69  
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Active-Site 132  
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;
Sequence-Conflict 231  
[BroomeSmith88, UniProt10a]
Alternate sequence: V → E; UniProt: (in Ref. 1; CAA29775);
Amino-Acid-Sites-That-Bind 235  
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Transmembrane-Region 379 -> 399 PBP6 transmembrane segment
[vanderLinden92]
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0839 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10203; confirmed by SwissProt match.


References

Aldea89: Aldea M, Garrido T, Hernandez-Chico C, Vicente M, Kushner SR (1989). "Induction of a growth-phase-dependent promoter triggers transcription of bolA, an Escherichia coli morphogene." EMBO J 8(12);3923-31. PMID: 2684651

Amanuma80: Amanuma H, Strominger JL (1980). "Purification and properties of penicillin-binding proteins 5 and 6 from Escherichia coli membranes." J Biol Chem 255(23);11173-80. PMID: 7002918

Amanuma84: Amanuma H, Strominger JL (1984). "Purification and properties of penicillin-binding proteins 5 and 6 from the dacA mutant strain of Escherichia coli (JE 11191)." J Biol Chem 259(2);1294-8. PMID: 6363404

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

Baquero96: Baquero MR, Bouzon M, Quintela JC, Ayala JA, Moreno F (1996). "dacD, an Escherichia coli gene encoding a novel penicillin-binding protein (PBP6b) with DD-carboxypeptidase activity." J Bacteriol 178(24);7106-11. PMID: 8955390

Begg90: Begg KJ, Takasuga A, Edwards DH, Dewar SJ, Spratt BG, Adachi H, Ohta T, Matsuzawa H, Donachie WD (1990). "The balance between different peptidoglycan precursors determines whether Escherichia coli cells will elongate or divide." J Bacteriol 172(12);6697-703. PMID: 2254246

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

BroomeSmith82: Broome-Smith JK, Spratt BG (1982). "Deletion of the penicillin-binding protein 6 gene of Escherichia coli." J Bacteriol 152(2);904-6. PMID: 6215397

BroomeSmith85: Broome-Smith JK (1985). "Construction of a mutant of Escherichia coli that has deletions of both the penicillin-binding protein 5 and 6 genes." J Gen Microbiol 131(8);2115-8. PMID: 3903044

BroomeSmith88: Broome-Smith JK, Ioannidis I, Edelman A, Spratt BG (1988). "Nucleotide sequences of the penicillin-binding protein 5 and 6 genes of Escherichia coli." Nucleic Acids Res 16(4);1617. PMID: 3279397

Buchanan82: Buchanan CE, Sowell MO (1982). "Synthesis of penicillin-binding protein 6 by stationary-phase Escherichia coli." J Bacteriol 151(1);491-4. PMID: 7045084

Denome99: Denome SA, Elf PK, Henderson TA, Nelson DE, Young KD (1999). "Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis." J Bacteriol 181(13);3981-93. PMID: 10383966

dePedro03: de Pedro MA, Young KD, Holtje JV, Schwarz H (2003). "Branching of Escherichia coli cells arises from multiple sites of inert peptidoglycan." J Bacteriol 185(4);1147-52. PMID: 12562782

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

Ghosh03: Ghosh AS, Young KD (2003). "Sequences near the active site in chimeric penicillin binding proteins 5 and 6 affect uniform morphology of Escherichia coli." J Bacteriol 185(7);2178-86. PMID: 12644487

Ghosh08: Ghosh AS, Chowdhury C, Nelson DE (2008). "Physiological functions of D-alanine carboxypeptidases in Escherichia coli." Trends Microbiol 16(7);309-17. PMID: 18539032

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."

Harris02: Harris F, Brandenburg K, Seydel U, Phoenix D (2002). "Investigations into the mechanisms used by the C-terminal anchors of Escherichia coli penicillin-binding proteins 4, 5, 6 and 6b for membrane interaction." Eur J Biochem 269(23);5821-9. PMID: 12444970

Harris97: Harris F, Phoenix DA (1997). "An investigation into the ability of C-terminal homologues of Escherichia coli low molecular mass penicillin-binding proteins 4, 5 and 6 to undergo membrane interaction." Biochimie 79(4);171-4. PMID: 9242980

Harris98b: Harris F, Demel R, de Kruijff B, Phoenix DA (1998). "An investigation into the lipid interactions of peptides corresponding to the C-terminal anchoring domains of Escherichia coli penicillin-binding proteins 4, 5 and 6." Biochim Biophys Acta 1415(1);10-22. PMID: 9858668

Hayes06: Hayes ET, Wilks JC, Sanfilippo P, Yohannes E, Tate DP, Jones BD, Radmacher MD, BonDurant SS, Slonczewski JL (2006). "Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12." BMC Microbiol 6;89. PMID: 17026754

Holtje98: Holtje JV (1998). "Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli." Microbiol Mol Biol Rev 62(1);181-203. PMID: 9529891

Hsieh06: Hsieh ML, Tseng MJ, Tseng MC, Chu YH (2006). "Identification of a new chromophoric substrate in the library of amino acid p-nitroanilides for continuous assay of VanX, a D,D-dipeptidase essential for vancomycin resistance." Anal Biochem 354(1);104-10. PMID: 16701071

Josephine06: Josephine HR, Charlier P, Davies C, Nicholas RA, Pratt RF (2006). "Reactivity of penicillin-binding proteins with peptidoglycan-mimetic beta-lactams: what's wrong with these enzymes?." Biochemistry 45(51);15873-83. PMID: 17176110

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

Lange91a: Lange R, Hengge-Aronis R (1991). "Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S." J Bacteriol 173(14);4474-81. PMID: 1648559

Laubacher08: Laubacher ME, Ades SE (2008). "The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance." J Bacteriol 190(6);2065-74. PMID: 18192383

Leidenix89: Leidenix MJ, Jacoby GH, Henderson TA, Young KD (1989). "Separation of Escherichia coli penicillin-binding proteins into different membrane vesicles by agarose electrophoresis and sizing chromatography." J Bacteriol 171(10);5680-6. PMID: 2676988

Matsuhashi79: Matsuhashi M, Tamaki S, Curtis SJ, Strominger JL (1979). "Mutational evidence for identity of penicillin-binding protein 5 in Escherichia coli with the major D-alanine carboxypeptidase IA activity." J Bacteriol 137(1);644-7. PMID: 368033

Meberg01: Meberg BM, Sailer FC, Nelson DE, Young KD (2001). "Reconstruction of Escherichia coli mrcA (PBP 1a) mutants lacking multiple combinations of penicillin binding proteins." J Bacteriol 183(20);6148-9. PMID: 11567017

Nanninga98: Nanninga N (1998). "Morphogenesis of Escherichia coli." Microbiol Mol Biol Rev 62(1);110-29. PMID: 9529889

Nelson00: Nelson DE, Young KD (2000). "Penicillin binding protein 5 affects cell diameter, contour, and morphology of Escherichia coli." J Bacteriol 182(6);1714-21. PMID: 10692378

Nelson01: Nelson DE, Young KD (2001). "Contributions of PBP 5 and DD-carboxypeptidase penicillin binding proteins to maintenance of cell shape in Escherichia coli." J Bacteriol 183(10);3055-64. PMID: 11325933

Nelson02: Nelson DE, Ghosh AS, Paulson AL, Young KD (2002). "Contribution of membrane-binding and enzymatic domains of penicillin binding protein 5 to maintenance of uniform cellular morphology of Escherichia coli." J Bacteriol 184(13);3630-9. PMID: 12057958

Obermann94: Obermann W, Holtje JV (1994). "Alterations of murein structure and of penicillin-binding proteins in minicells from Escherichia coli." Microbiology 140 ( Pt 1);79-87. PMID: 8162193

Pratt81: Pratt JM, Boulnois GJ, Darby V, Orr E, Wahle E, Holland IB (1981). "Identification of gene products programmed by restriction endonuclease DNA fragments using an E. coli in vitro system." Nucleic Acids Res 9(18);4459-74. PMID: 6272207

Pratt81a: Pratt JM, Holland IB, Spratt BG (1981). "Precursor forms of penicillin-binding proteins 5 and 6 of E. coli cytoplasmic membrane." Nature 293(5830);307-9. PMID: 7024823

Rawlings93: Rawlings ND, Barrett AJ (1993). "Evolutionary families of peptidases." Biochem J 290 ( Pt 1);205-18. PMID: 8439290

Santos02: Santos JM, Lobo M, Matos AP, De Pedro MA, Arraiano CM (2002). "The gene bolA regulates dacA (PBP5), dacC (PBP6) and ampC (AmpC), promoting normal morphology in Escherichia coli." Mol Microbiol 45(6);1729-40. PMID: 12354237

Scheffers05: Scheffers DJ, Pinho MG (2005). "Bacterial cell wall synthesis: new insights from localization studies." Microbiol Mol Biol Rev 69(4);585-607. PMID: 16339737

Siligardi97: Siligardi G, Harris F, Phoenix DA (1997). "Alpha-helical conformation in the C-terminal anchoring domains of E. coli penicillin-binding proteins 4, 5 and 6." Biochim Biophys Acta 1329(2);278-84. PMID: 9371419

Spratt77: Spratt BG (1977). "Properties of the penicillin-binding proteins of Escherichia coli K12,." Eur J Biochem 72(2);341-52. PMID: 319999

Spratt80: Spratt BG, Boyd A, Stoker N (1980). "Defective and plaque-forming lambda transducing bacteriophage carrying penicillin-binding protein-cell shape genes: genetic and physical mapping and identification of gene products from the lip-dacA-rodA-pbpA-leuS region of the Escherichia coli chromosome." J Bacteriol 143(2);569-81. PMID: 6451612

Stefanova02: Stefanova ME, Davies C, Nicholas RA, Gutheil WG (2002). "pH, inhibitor, and substrate specificity studies on Escherichia coli penicillin-binding protein 5." Biochim Biophys Acta 1597(2);292-300. PMID: 12044907

Tamura76: Tamura T, Imae Y, Strominger JL (1976). "Purification to homogeneity and properties of two D-alanine carboxypeptidases I From Escherichia coli." J Biol Chem 251(2);414-23. PMID: 1391

Tani02: Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG (2002). "Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis." Proc Natl Acad Sci U S A 99(21);13471-6. PMID: 12374860

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.

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

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."

vanderLinden92: van der Linden MP, de Haan L, Hoyer MA, Keck W (1992). "Possible role of Escherichia coli penicillin-binding protein 6 in stabilization of stationary-phase peptidoglycan." J Bacteriol 174(23);7572-8. PMID: 1447130

Varma04: Varma A, Young KD (2004). "FtsZ collaborates with penicillin binding proteins to generate bacterial cell shape in Escherichia coli." J Bacteriol 186(20);6768-74. PMID: 15466028

Waxman82: Waxman DJ, Amanuma H, Strominger JL (1982). "Amino acid sequence homologies between Escherichia coli penicillin-binding protein 5 and class A beta-lactamases." FEBS Lett 139(2);159-63. PMID: 7042389

Other References Related to Gene Regulation

Guinote11: Guinote IB, Matos R, Freire P, Arraiano C (2011). "BolA Affects Cell Growth, and Binds to the Promoters of Penicillin-Binding Proteins 5 and 6 and Regulates Their Expression." J Microbiol Biotechnol 21(3);243-51. PMID: 21464593

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Raivio13: Raivio TL, Leblanc SK, Price NL (2013). "The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity." J Bacteriol 195(12);2755-67. PMID: 23564175


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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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