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MetaCyc Enzyme: fused 4'-phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase

Gene: dfp Accession Numbers: EG10004 (MetaCyc), b3639, ECK3629

Synonyms: coaBC

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of fused 4'-phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase = [Dfp]12

Summary:
The dfp (coaBC) gene encodes a bifunctional protein that catalyzes two sequential reactions in the coenzyme A biosynthetic pathway [Strauss01, Kupke01, Kupke00]. The C-terminal ("CoaB") domain of the protein confers phosphopantothenoylcysteine synthetase activity; CoaB alone forms dimers in solution [Kupke02], and crystal structures of this domain have been solved [Stanitzek04]. The N-terminal ("CoaC") domain of the protein binds FMN and confers 4'-phosphopantothenoylcysteine decarboxylase activity [Kupke00, Kupke01]. The domain can be expressed separately and forms dodecamers [Kupke01].

The existence of a 4'-phosphopantothenoyl-CMP intermediate in the synthetase reaction has been confirmed [Kupke04].

A pathway for formation of the substrate-activating thioaldehyde for the decarboxylation reaction has been proposed [Strauss01a], and the stereochemistry of the reaction has been studied [Strauss03].

dfp is an essential gene [Gerdes02]. A temperature-sensitive allele has been isolated [Spitzer85].

Locations: cytosol

Map Position: [3,810,754 -> 3,811,974]

Molecular Weight of Polypeptide: 43.438 kD (from nucleotide sequence), 45.0 kD (experimental) [Spitzer85 ]

Molecular Weight of Multimer: 600.0 kD (experimental) [Kupke00]

Unification Links: ASAP:ABE-0011896 , CGSC:18430 , DIP:DIP-48472N , EchoBASE:EB0004 , EcoGene:EG10004 , EcoliWiki:B3639 , OU-Microarray:b3639 , PortEco:dfp , PR:PRO_000022309 , Pride:P0ABQ0 , Protein Model Portal:P0ABQ0 , RefSeq:NP_418096 , RegulonDB:EG10004 , SMR:P0ABQ0 , String:511145.b3639 , UniProt:P0ABQ0

Relationship Links: InterPro:IN-FAMILY:IPR003382 , InterPro:IN-FAMILY:IPR005252 , InterPro:IN-FAMILY:IPR007085 , PDB:Structure:1U7U , PDB:Structure:1U7W , PDB:Structure:1U7Z , PDB:Structure:1U80 , Pfam:IN-FAMILY:PF02441 , Pfam:IN-FAMILY:PF04127

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0015937 - coenzyme A biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01, Strauss01]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0015941 - pantothenate catabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0004632 - phosphopantothenate--cysteine ligase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Strauss01]
GO:0004633 - phosphopantothenoylcysteine decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Kupke00]
GO:0010181 - FMN binding Inferred from experiment Inferred by computational analysis [GOA01, Kupke00, Spitzer85]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016831 - carboxy-lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers Coenzyme A and its modification

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: phosphopantothenoylcysteine synthetase

Synonyms: phosphopantothenate-cysteine ligase, (R)-4'-phosphopantothenate:L-cysteine ligase, P-pantothenate cysteine ligase

EC Number: 6.3.2.5

(R)-4'-phosphopantothenate + L-cysteine + CTP <=> R-4'-phosphopantothenoyl-L-cysteine + CMP + diphosphate + H+

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.

In Pathways: pantothenate and coenzyme A biosynthesis I , coenzyme A biosynthesis I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactors or Prosthetic Groups: Mg2+ [Strauss01]

Inhibitors (Unknown Mechanism): (R)-4'-phosphopantothenate [Strauss01, Comment 1]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-cysteine
240.0
[Strauss01]
CTP
290.0
[Strauss01]
(R)-4'-phosphopantothenate
290.0
[Strauss01]


Enzymatic reaction of: 4'-phosphopantothenoylcysteine decarboxylase

Synonyms: phosphopantothenoylcysteine decarboxylase, N-((R)-4-phosphopantothenoyl)-L-cysteine carboxy-lyase, P-pantothenoylcysteine decarboxylase

EC Number: 4.1.1.36

R-4'-phosphopantothenoyl-L-cysteine + H+ <=> 4'-phosphopantetheine + CO2

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.

In Pathways: pantothenate and coenzyme A biosynthesis I , coenzyme A biosynthesis I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactors or Prosthetic Groups: FMN [Kupke00]

Kinetic Parameters:

Substrate
Km (μM)
Citations
R-4'-phosphopantothenoyl-L-cysteine
780.0
[Strauss01]


Sequence Features

Feature Class Location Catalytic Activity Citations Comment
Cleavage-of-Initial-Methionine 1  
[Kupke00, Ge02]
 
Protein-Segment 2 -> 188  
[UniProt10]
UniProt: Phosphopantothenoylcysteine decarboxylase; Sequence Annotation Type: region of interest;
Chain 2 -> 406  
[UniProt09]
UniProt: Coenzyme A biosynthesis bifunctional protein coaBC;
Catalytic-Domain 2 -> 190 4'-phosphopantothenoylcysteine decarboxylase
[Kupke00, Kupke01]
 
Mutagenesis-Variant 11  
[Kupke01, UniProt11]
Alternate sequence: D; UniProt: In Dfp-707; temperature-sensitive, impairs folding.
Mutagenesis-Variant 14  
[Kupke01, UniProt11]
Alternate sequence: S; UniProt: No FMN binding.
Mutagenesis-Variant 15  
[Kupke01, UniProt11]
Alternate sequence: A; UniProt: Less than 5% of wild-type activity.
Mutagenesis-Variant 16  
[Kupke01, UniProt11]
Alternate sequence: V; UniProt: Slightly reduced activity.
Alternate sequence: L; UniProt: Severely reduced activity.
Mutagenesis-Variant 17  
[Kupke01, UniProt11]
Alternate sequence: S; UniProt: Almost wild-type activity.
Alternate sequence: G; UniProt: Almost wild-type activity.
Alternate sequence: D; UniProt: Less than 5% of wild-type activity.
Mutagenesis-Variant 19  
[Kupke01, UniProt11]
Alternate sequence: L; UniProt: Reduced activity.
Alternate sequence: F; UniProt: Almost wild-type activity.
Mutagenesis-Variant 20  
[Kupke01, UniProt11]
Alternate sequence: R; UniProt: Almost wild-type activity.
Alternate sequence: Q; UniProt: Reduced activity.
Alternate sequence: N; UniProt: Reduced activity.
Mutagenesis-Variant 46  
[Kupke00, UniProt11]
Alternate sequence: L; UniProt: Reduced activity.
Mutagenesis-Variant 75  
[Kupke00, UniProt11]
Alternate sequence: N; UniProt: Loss of activity.
Mutagenesis-Variant 89  
[Kupke00, UniProt11]
Alternate sequence: D; UniProt: No FMN binding.
Alternate sequence: A; UniProt: Binds FMN, but more loosely than wild-type.
Mutagenesis-Variant 91  
[Kupke00, UniProt11]
Alternate sequence: V; UniProt: Binds FMN.
Mutagenesis-Variant 124  
[Kupke00, UniProt11]
Alternate sequence: L; UniProt: No effect.
Mutagenesis-Variant 125  
[Kupke01, Kupke00, UniProt11]
Alternate sequence: Q; UniProt: Loss of activity.
Alternate sequence: D; UniProt: Loss of activity.
Amino-Acid-Sites-That-Bind 125  
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 128  
[Kupke00, UniProt11]
Alternate sequence: L; UniProt: Severely reduced activity.
Mutagenesis-Variant 158  
[UniProt10a]
Alternate sequence: S; UniProt: Loss of activity;
Alternate sequence: A; UniProt: Loss of activity;
Active-Site 158  
[UniProt10]
UniProt: Proton donor; Non-Experimental Qualifier: probably;
Protein-Segment 189 -> 406  
[UniProt10]
UniProt: Phosphopantothenate--cysteine ligase; Sequence Annotation Type: region of interest;
Catalytic-Domain 191 -> 406 phosphopantothenoylcysteine synthetase
[Kupke01, Kupke02]
 
Mutagenesis-Variant 194  
[Kupke02, UniProt11]
Alternate sequence: V; UniProt: Loss of dimerization.
Mutagenesis-Variant 198  
[Kupke02, UniProt11]
Alternate sequence: V; UniProt: Loss of dimerization.
Mutagenesis-Variant 203  
[Kupke02, UniProt11]
Alternate sequence: N; UniProt: Loss of dimerization.
Mutagenesis-Variant 210  
[Kupke04, Kupke02, UniProt11]
Alternate sequence: K; UniProt: Loss of activity, reaction intermediate not detectable.
Alternate sequence: H; UniProt: Loss of activity, reaction intermediate not detectable.
Alternate sequence: D; UniProt: Loss of activity, reaction intermediate detectable.
Mutagenesis-Variant 212  
[Kupke02, UniProt11]
Alternate sequence: A; UniProt: Small effect on activity.
Mutagenesis-Variant 215  
[Kupke02, UniProt11]
Alternate sequence: Q; UniProt: No effect.
Mutagenesis-Variant 275  
[Kupke04, Kupke02, UniProt11]
Alternate sequence: V; UniProt: Loss of dimerization.
Amino-Acid-Sites-That-Bind 279  
[UniProt10a]
UniProt: CTP;
Mutagenesis-Variant 289  
[Kupke02, UniProt11]
Alternate sequence: Q; UniProt: Loss of activity.
Amino-Acid-Sites-That-Bind 289  
[UniProt10a]
UniProt: CTP;
Mutagenesis-Variant 291  
[Kupke02, UniProt11]
Alternate sequence: Q; UniProt: Reduced activity.
Mutagenesis-Variant 292  
[Kupke02, UniProt11]
Alternate sequence: Q; UniProt: Small effect on activity.
Amino-Acid-Sites-That-Bind 341  
[UniProt10a]
UniProt: CTP;
Amino-Acid-Sites-That-Bind 345  
[UniProt10a]
UniProt: CTP;

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3639 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10004; confirmed by SwissProt match.


References

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

Ge02: Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP, McLafferty FW (2002). "Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry." J Am Chem Soc 124(4);672-8. PMID: 11804498

Gerdes02: Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, Osterman AL (2002). "From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways." J Bacteriol 184(16);4555-72. PMID: 12142426

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kupke00: Kupke T, Uebele M, Schmid D, Jung G, Blaesse M, Steinbacher S (2000). "Molecular characterization of lantibiotic-synthesizing enzyme EpiD reveals a function for bacterial Dfp proteins in coenzyme A biosynthesis." J Biol Chem 2000;275(41);31838-46. PMID: 10922366

Kupke01: Kupke T (2001). "Molecular characterization of the 4'-phosphopantothenoylcysteine decarboxylase domain of bacterial Dfp flavoproteins." J Biol Chem 2001;276(29);27597-604. PMID: 11358972

Kupke02: Kupke T (2002). "Molecular characterization of the 4'-phosphopantothenoylcysteine synthetase domain of bacterial dfp flavoproteins." J Biol Chem 277(39);36137-45. PMID: 12140293

Kupke04: Kupke T (2004). "Active-site residues and amino acid specificity of the bacterial 4'-phosphopantothenoylcysteine synthetase CoaB." Eur J Biochem 271(1);163-72. PMID: 14686929

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Spitzer85: Spitzer ED, Weiss B (1985). "dfp Gene of Escherichia coli K-12, a locus affecting DNA synthesis, codes for a flavoprotein." J Bacteriol 164(3);994-1003. PMID: 2999089

Stanitzek04: Stanitzek S, Augustin MA, Huber R, Kupke T, Steinbacher S (2004). "Structural basis of CTP-dependent peptide bond formation in coenzyme A biosynthesis catalyzed by Escherichia coli PPC synthetase." Structure 12(11);1977-88. PMID: 15530362

Strauss01: Strauss E, Kinsland C, Ge Y, McLafferty FW, Begley TP (2001). "Phosphopantothenoylcysteine synthetase from Escherichia coli. Identification and characterization of the last unidentified coenzyme A biosynthetic enzyme in bacteria." J Biol Chem 2001;276(17);13513-6. PMID: 11278255

Strauss01a: Strauss E, Begley TP (2001). "Mechanistic studies on phosphopantothenoylcysteine decarboxylase." J Am Chem Soc 123(26);6449-50. PMID: 11427085

Strauss03: Strauss E, Begley TP (2003). "Stereochemical studies on phosphopantothenoylcysteine decarboxylase from Escherichia coli." Bioorg Med Chem Lett 13(3);339-42. PMID: 12565925

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."

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Nov 23, 2014, BIOCYC14A.